% goss(1) Gossamer User Manual % Bryan Beresford-Smith, Andrew Bromage, Thomas Conway, Jeremy Wazny, Justin Zobel % March 28, 2012

NAME

goss - a tool for de novo assembly of high throughput sequencing data.

Version 1.3.0

SYNOPSIS

goss build-graph -k 27 -i in.fastq -O graph

goss merge-graphs -G graph1 -G graph2 -O graph-merged

goss trim-graph -G graph -O graph-trimmed

goss prune-tips -G graph -O graph-pruned

goss print-contigs --min-coverage 10 --min-length 100 -G graph-pruned > paths.fa

goss pop-bubbles -G graph-pruned -O graph-popped

goss build-entry-edge-set -G graph-popped

goss build-supergraph -C 10 -G graph-popped

goss thread-pairs -G graph-popped --expected-coverage 70 --insert-expected-length 300

goss thread-reads -G graph-popped --expected-coverage 70

goss build-scaffold -G graph-popped --expected-coverage 70 --insert-expected-length 300

goos scaffold -G graph-popped

DESCRIPTION

Gossamer is an application for doing de novo assembly of high throughput sequencing data. It is a memory efficient assembler based on the de Bruijn graph.

The advantage of Gossamer is that large data sets can be assembled on computers with small amounts of memory. The fundamental parameter to de Bruijn graph based methods is k, the size of substrings used in the construction of the graph. These substrings are referred to as k-mers and correspond to nodes in the graph. Edges in the graph correspond to (k+1)-mers which are called rho-mers. It should be noted that larger values of k will require larger memory sizes because the size of the rho-mer space is larger. Another point to note is that by using a small cluster of small memory computers the time can be easily and substantially reduced by building subsections of the graph in parallel.

Input files are base-space reads in FASTA or FASTQ format or in a format with one read per line and in either plain text or compressed format (i.e. gzip).

Using Gossamer

Gossamer runs in several phases and each phase will produce a new graph or additional information for an existing graph. Graphs are represented as a collection of files with a common prefix which may include a filesystem path. For example, the files composing a graph object with prefix "graph" are:

graph-counts-hist.txt
graph-counts.ord0
graph-counts.ord1
graph-counts.ord1p.classes
graph-counts.ord1p.class-sum
graph-counts.ord1p.header
graph-counts.ord1p.offsets
graph-counts.ord1p.offset-sum
graph-counts.ord2
graph-counts.ord2p.classes
graph-counts.ord2p.class-sum
graph-counts.ord2p.header
graph-counts.ord2p.offsets
graph-counts.ord2p.offset-sum
graph-edges-d0
graph-edges-d1
graph-edges.header
graph-edges.high-bits
graph-edges.low-bits.lwr
graph-edges.low-bits.upr
graph.header

It is currently up to the user to organize the names of graphs in a meaningful way. See the example of the common phases of goss given below.

Any graph can be processed to find the contigs in the graph and to output those contigs to a FASTA file (or stdout). Various statistics for each contig are included in the contig description line, including the identifier of the contig, its length and information about the rho-mer coverage. The rho-mer coverage is the number of times the rho-mer occurs in the set of reads and for each printed contig the minimum, maximum, mean and standard deviation of the coverage in the contig is given.

One of the files representing the graph is a text file called <prefix>-counts-hist.txt, each line of which consists of a pair (x, y) where y is the number of different rho-mers which occur exactly x times. This information is useful for determining the minimum multiplicity to use for trimming the graph (see below).

As an example of using gossamer, suppose the sequenced reads are in four files, three of which are FASTQ files (one of which is compressed) and one of which is a FASTA file: in1.fastq, in2.fastq.gz, in3.fastq and in4.fasta.

The common phases of gossamer are:

Build the complete de Bruijn graph for some k-mer size using all of the read data
- If the data consists of several files e.g. from different lanes of sequencing then it is recommended that goss build-graph be run on each file separately and the resulting graphs merged using goss merge-graphs.
goss build-graph -k 27 -i in1.fastq -i in2.fastq.gz -O graph1

goss build-graph -k 27 -i in3.fastq -I in4.fasta -O graph2

goss merge-graphs -G graph1 -G graph2 -O graph12-merged
Trim all rho-mers with low frequency from the complete graph.
- Rho-mers with low frequency arise overwhelmingly from sequencing errors, at least if there is good genome coverage. By default, Gossamer will automatically choose an appropriate cut-off frequency which eliminates as many of these incorrect rho-mers while keeping as it can while keeping as many correct rho-mers as possible.
- Under some circumstances, for example if the coverage is low, the user may need to supply an appropriate cut-off frequency using the -C parameter. To pick an appropriate cut-off frequency, it may be necessary to inspect the histogram of rho-mer counts in the graph which has been built from all of the reads. For this example, the file containing this histogram would be called graph12-merged-counts-hist.txt.
goss trim-graph -G graph12-merged -O graph12-merged-trimmed
Prune the tips of the trimmed graph using goss prune-tips, to clean up additional edges resulting from sequencing errors.

goss prune-tips -G graph12-merged-trimmed -O graph12-merged-trimmed-pruned1
Repeat the pruning since one step of pruning can create further tips which can be removed. This can be done until sufficiently small numbers of new tips are discovered, or even until no more tips are discovered.

goss prune-tips -G graph12-merged-trimmed-pruned1 -O graph12-merged-trimmed-pruned2
Output the contigs to a FASTA file.
- At this stage of the assembly, all of the read data has been incorporated into a de Bruijn graph and that graph has been substantially cleaned of features arising from read errors. It is now possible to print all of the unbranched paths in the graph even though further steps in the assembly process will most likely substantially improve the overall lengths of the contigs. In fact, at any point in the graph building, e.g. after pruning, these contigs can be printed.
goss print-contigs --min-coverage 10 --min-length 100 -G graph12-merged-trimmed-pruned2 -o paths.fa
Pop the "bubbles" in the graph.
- A "bubble" is a graph structure with two similar, alternative paths between a start and an end for which the paths are not too long. These paths may arise, for example, because of the heterozygous nature of a diploid genome, sequencing errors, or by variants such as SNPs or cloning artifacts. It can be beneficial during the assembly process to remove one of the two alternative paths. The pop-bubbles command detects such "bubbles" and removes them from the graph.
goss pop-bubbles -G graph12-merged-trimmed-pruned2 -O graph12-merged-trimmed-pruned2-popped
Build the graph entry edge sets.
- After the initial filtering steps described above, pairs of reads can be used to extend the contigs by resolving repeat structures. A new graph which we call a supergraph is constructed and manipulated during this process. The supergraph structure, which is not itself a de Bruijn graph, is stored beside the original de Bruijn graph, which remains unmodified.
  
  There are three stages to this process: 1. Build the entry edge sets. 2. Build a supergraph from the established linear segments. 3. Resolve paths corresponding to pairs of reads.
  
  As a first stage, a set of entry edge sets is constructed for the graph. These identify the beginnings of (unbranching) linear segments in the de Bruijn graph.
goss build-entry-edge-sets -G graph12-merged-trimmed-pruned2-popped
Build the initial supergraph.
- Once the entry edge sets have been constructed the information can be used to build the de Bruijn graph's supergraph. Note that no explicit name is provided for the new graph: in later commands, the supergraph is identified by reference to the de Bruijn graph from which it was generated.
goss build-supergraph -G graph12-merged-trimmed-pruned2-popped
Use read pairs to resolve repeat structures.
- The initial supergraph represents all of the unbranching segments of the de Bruijn graph. Paired read information can be used to establish which of the many possible paths through the graph correspond to true sequences of the original genome. Gossamer requires read pairs to be supplied as a pair of files; the nth reads of the first and the second input files make up the nth read pair. Both paired-end and mate-pair formats are supported. Additionally, the estimated genome coverage of the original de Bruijn graph, and the expected pair insert size must be provided. The result of "threading" pairs is a supergraph which is updated in-place. The pair threading step may be run multiple times, with different inputs and metadata, resulting in a more refined supergraph after each step. Note that, at any stage the supergraph can be restored to its initial state by re-running the build-supergraph command.
goss thread-pairs -G graph12-merged-trimmed-pruned2 -i in1.fastq -i in2.fastq --insert-expected-size 200 --expected-coverage 70
Use individual reads to resolve remaining small-scale repeat structures
- Just as read pairs are used to join distant contigs, individual reads may be used to connect contigs which are spanned by individual reads. The read threading step operates on the same supergraph, updating it in place, in the same way as pair threading. It also requires an expected coverage estimate.
goss thread-reads -G graph12-merged-trimmed-pruned2 -i in1.fastq -i in2.fastq --expected-coverage 70
Use read pairs to order and join unique contigs.
- Long subsequences of the genome may appear as disconnected segments of the supergraph. Read pair information can be used to order and orient these sequences, yielding longer contigs. This process is known as scaffolding. Gossamer performs scaffolding in two steps: first the scaffold link graphs must be constructed from the pair libraries, then these scaffolds can be applied to the supergraph, updating it in place.
goss build-scaffold -G graph12-merged-trimmed-pruned2 --mate-pairs -i in1.fastq -i in2.fastq --insert-expected-size 3500 --expected-coverage 70

goss scaffold -G graph12-merged-trimmed-pruned2
Print the supergraph contigs.
- Once the supergraph has been built, including after any pair/read threading or scaffolding step, the contigs can be printed in FASTA format.
goss print-contigs --min-length 100 -G graph12-merged-trimmed-pruned2-popped -o supergraphContigs.fa

OPTIONS COMMON TO ALL COMMANDS

The following options can be used with all of the goss commands and are therefore not listed separately for each command.

-h, --help : Show a help message.

-l FILE, --log-file FILE : Place to write progress messages. Messages are only written if the -v flag is used. If omitted, messages are written to stderr.

-T INT, --num-threads INT : The maximum number of worker threads to use. The actual number of threads used during the algorithms depends on each implementation. goss may use a small number of additional threads for performing non cpu-bound operations, such as file I/O.

--tmp-dir DIRECTORY : A directory to use for temporary files. This flag may be repeated in order to nominate multiple temporary directories.

-v, --verbose : Show progress messages.

-V, --version : Show the software version.

-D arg, --debug arg : Enable particular debugging output.

COMMANDS AND OPTIONS

goss build-graph

goss build-graph [-B INT] [-S INT] -k INT {-I FASTA-filename | -i FASTQ-filename | --line-in filename}+ -O PREFIX

Build the de Bruijn graph from the reads contained in the given FASTA and FASTQ files and output the resulting graph object as a set of files with the given PREFIX. Both FASTA and FASTQ input files are supported, with options -I and -i respectively.
In addition, files with one read per line are also supported. The input files can be compressed with the compression method implied by the file suffix as follows:

.gz Compressed using gzip.

For large projects (such as sequencing the human genome with high coverage) several separate goss build-graph commands may be done on different files in parallel (e.g. on files from different lanes of an Illumina GAII), followed by a sequence of merging steps using goss merge-graphs. Even in the absence of a cluster, building parts and merging is usually faster than building a large graph with all the input files in one go. Future releases may do this automatically.

OPTIONS

-B INT, --buffer-size INT : Maximum buffer-size for in-memory buffers is INT Gigabytes (defaults to 2). This is a convenient way of setting the maximum amount of RAM which will be used by build-graph and
allows build-graph to be run on machines with a small amount of memory.
For large data sets, however, larger values for B will improve performance. For example, for a data set with a large number (e.g. 70 million) of reads of length 100, a typical value of B would be 24 (i.e. use 24 Gb buffers). The actual optimal value for the buffer-size is related to the final graph size. A typical value for B would be the amount of machine RAM, in Gigabytes. Note: In the current release this must be less than 88.

-I FILE, --fasta-in FILE : Input file in FASTA format.

-i FILE, --fastq-in FILE : Input file in FASTQ format.

--line-in FILE : Input file with one read per line and no other annotation.

-O PREFIX, --graph-out PREFIX : Use PREFIX as the prefix name of the output graph object. The PREFIX must be a valid file name prefix.

-k INT, --kmer-size INT : The k-mer size to use for building the graph: in version 0.3.0 this must be an integer strictly less than 63.

goss help

Prints a summary of all of the gossamer commands.

goss lint-graph

goss lint-graph {-G | --graph-in} PREFIX

Report any inconsistencies in the graph. This includes a check of the symmetry of paths and their reverse complements in the graph.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the graph object. This is the string used as the prefix for the names of the files making up a graph object.

goss merge-graphs

goss merge-graphs {-G PREFIX}+ -O PREFIX

Create a new graph by merging one or more other graphs.

Merging uses a small, constant amount of memory per graph; very likey less than 1 GB of memory in total.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the graph object. This is the string used as the prefix for the names of the files making up a graph object. When merging several graphs this parameter is repeated for each graph, as demonstrated in the example above.

-O PREFIX, --graph-out PREFIX : Use PREFIX as the prefix name of the output graph object. The PREFIX must be a valid file name prefix.

goss print-contigs

goss print-contigs -G PREFIX [--min-coverage INT] [--min-length INT] [-o FILE] [--no-sequence] [--verbose-headers] [--no-line-breaks] [--include-entailed-contigs] [--print-rcs]

Print all of the non-branching paths in a given graph. By default, contigs will be printed from the supergraph if it is present, otherwise the de Bruijn graph will be used. The paths are printed in FASTA format with a uniquely identify integer in each contig's header/descriptor line. If the --verbose-headers flag is supplied, additional information about contigs will be added to each header. The make up of a 'verbose' header depends on whether the underlying graph is a de Bruijn graph or a supergraph. In the case of a de Bruijn graph, the header line contains the following additional information (interspersed with colons ':'), which is separated from the contig id number by a space:

Path Length
Minimum Path Coverage
Maximum Path Coverage
Average Path Coverage
Standard Deviation of Path Coverage

The coverage of a rho-mer is defined to be the number of times it occurs in all reads. The minimum path coverage is the minimum coverage of all of the rho-mers in the path.

For contigs generated from a supergraph, the descriptor line is made up of the following fields (separated by commas ','):

Path Length
List of Segment Lengths (separated by colons ':')
List of Segment Starts (separated by colons ':')
The Integer Identifier of the Reverse Complement
List of Integer Identifiers of Successor Segments in the Supergraph (separated by colons ':')
Minimum Path Coverage
Maximum Path Coverage
Average Path Coverage
Standard Deviation of Path Coverage

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the graph object. This is the string used as the prefix for the names of the files making up a graph object.

--min-coverage INT : Only print those paths which have a minimum rho-mer coverage >= C. This flag is only used when printing contigs from a de Bruijn graph. Defaults to 0.

--min-length INT : Only print those paths which have a length >= the specified minimum length. Defaults to 0.

-o FILE, --output-file FILE : The name of the FASTA output file for the printed paths. Use '-' to output to standard output. The FILE must be a valid file name. Defaults to standard output.

--no-sequence : Suppresses the printing of the actual contig sequences. Instead, only the information present in the (verbose) descriptor lines will be printed in a tab separated format. The default is to print sequences.

--print-linear-segments : Only print linear segments, ignoring the supergraph if it is present. The default is to use the supergraph if available.

--verbose-headers : Print extra information about each contig in its header/descriptor line (in addition to its uniquely identifying integer.)

--no-line-breaks : Print each contig on a single line, instead of breaking at 60 columns.

--include-entailed-contigs : By default, only supergraph contigs which are not completely contained within other contigs are printed. Supplying this flag results in all supergraph contigs being printed, regardless of whether they have been used in the construction of longer contigs. Note: Most long contigs, when combined into longer contigs, will be removed from the supergraph anyway, leaving only relatively short entailed contigs (< ~50 bases).

--print-rcs : Include each contig's reverse complement in the output.

goss prune-tips

Create a new graph by pruning the tips in the input graph. Pruning tips is the process of removing short dead-ends in the graph. It is probable that such graph features arise from errors in the reads.

goss prune-tips -G PREFIX -O PREFIX

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the input graph. This is the string used as the prefix for the names of the files making up a graph object.

-O PREFIX, --graph-out PREFIX : The name of the output graph. Use PREFIX as the prefix name of the output graph object. The PREFIX must be a valid file name prefix.

goss trim-graph

goss trim-graph [-C INT] -G PREFIX -O PREFIX

Create a new graph by trimming the input graph. Trimming is the process of removing all edges in the graph which occur less than times. This is used to remove those edges which most likely arose from errors.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the input graph. This is the string used as the prefix for the names of the files making up a graph object.

-O PREFIX, --graph-out PREFIX : The name of the output graph. Use PREFIX as the prefix name of the output graph object. The PREFIX must be a valid file name prefix.

-C INT, --cutoff INT : Edges with coverage at or below this value are removed.

goss pop-bubbles

goss pop-bubbles [--max-edit-distance INT] [--max-=error-rate FLOAT] [--max-sequence-length INT] -G PREFIX -O PREFIX

A "bubble" is a graph structure with two alternative paths between a start and an end vertex for which the paths are similar but not too long. These paths may arise, for example, because of the heterozygous nature of a diploid genome, sequencing errors, or by variants such as SNPs or cloning artifacts. It can be beneficial during the assembly process to remove one of the two alternative paths. pop-bubbles detects "bubbles" and removes them from the graph.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the input graph. This is the string used as the prefix for the names of the files making up a graph object.

-O PREFIX, --graph-out PREFIX : The name of the output graph. Use PREFIX as the prefix name of the output graph object. The PREFIX must be a valid file name prefix.

--max-edit-distance INT : The maximum edit distance to qualify as a bubble.

--max-error-rate FLOAT : The maximum error rate to qualify as a bubble.

--max-sequence-length INT : the maximum length of a sequence to consider.

goss build-entry-edge-set

goss build-entry-edge-sets -G PREFIX

Build the graph entry edge sets. The entries are represented by files with prefix PREFIX-entries.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the input graph. This is the string used as the prefix for the names of the files making up a graph object.

goss build-supergraph

goss build-supergraph -G PREFIX

Build the supergraph. The graph with the specified prefix is augmented with further files representing the supergraph.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the input graph. This is the string used as the prefix for the names of the files making up a graph object.

--delete-scaffold : By default, build-supergraph will not proceed if there are unapplied scaffold files from a previous run of build-scaffold present, e.g. because the scaffold command has not been run. This flag causes it to instead delete those files and continue.

goss thread-pairs

goss thread-pairs -G PREFIX {-I FASTA-filename | -i FASTQ-filename | --line-in filename}+ --expected-coverage INT --insert-expected-size INT [--insert-size-std-dev FLOAT] [--insert-size-tolerance FLOAT] [--min-link-count INT] [--search-radius INT] [--edge-cache-rate INT] [--paired-ends] [--mate-pairs] [--innies] [--outies]

This command locates pairs of reads on the supergraph and uses them to join sequences of branching segments into new, longer contigs. The first step is to identify pairs of contigs related by read pairs. goss finds and stores the supergraph location of both reads in each pair. We call each pair of reads which connects a pair of contigs, as well the position of those reads within the contigs, a link. Using the position information within a link, the distance between linked contigs is estimated. Pairs can be supplied in either paired-end or mate-pairs format.

Once all read pairs have been anchored to the graph, any contig pairs which do not have at least a minimal number of links are removed from consideration. For the remaining pairs, goss will attempt to find paths in the supergraph which join both sides of the pair. Only paths with lengths near the insert size are considered. The range of valid path lengths is specified by providing: the expected insert size; the size of a standard deviation, as a percentage of the insert size; and a tolerance value, which indicates the number of standard deviations in range. For example, specifying an insert size of 200 bases, a standard deviation of 10% and a tolerance of 2.0 standard deviations, means that only paths of length in the range [160,240] bases are considered. By default, goss will attempt to find all paths, between linked contigs, within the distance bounds. When a unique qualifying path is found, it is used to join the two sides of the corresponding contig pair, yielding a new, longer contig in their place. To improve performance, the area of the graph which is searched can be limited to within some distance of the target contig.

The result of running thread-pairs is a new supergraph, which is written over the top of the original. This command can be repeated for multiple sets of pairs, each of which will modify the same supergraph in-place.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the input graph. This is the string used as the prefix for the names of the files making up a graph object.

-I FILE, --fasta-in FILE : Input file in FASTA format.

-i FILE, --fastq-in FILE : Input file in FASTQ format.

--line-in FILE : Input file with one read per line and no other annotation.

--expected-coverate INT : The expected genome coverage of the reads used to build the underlying de Bruijn graph. These may or may not be the same as the read pairs used in this stage. This flag is mandatory.

--insert-expected-size INT : The insert size for the given pairs. i.e. the distance, in bases, between extreme ends of the pairs when mapped to the genome. This value must be supplied.

--insert-size-std-dev FLOAT : The standard deviation for allowed insert sizes, as a percentage. The default is 10%.

--insert-size-tolerance FLOAT : The range of valid insert sizes, in standard deviations. This defaults to 2.0.

--min-link-count INT : Disregard pairs of contigs which are linked by fewer than this number of read pairs. The default value is 10.

--search-radius INT : When searching for a path from one contig to another, limit the search to within this number of linear segments from the target. A radius value of 0 means that the search is not constrained to any region of the graph. Restricting path finding to an area of the graph is likely to decrease search times. There may be no noticeable benefit for relatively small graphs, however. The default value is 10.

--edge-cache-rate INT : To efficiently locate read pairs within the supergraph, goss builds a data structure for caching the positions of de Bruijn graph edge within the supergraph edges that contain them. In order to save memory, this information is stored for only a proportion of the complete set of de Bruijn graph edges. For a value of n, position information is stored for one edge out of every 2^n, where each entry takes 16 bytes. High values will reduce memory usage, at the expense of an increased runtime, while lower values will lower the runtime, but require more memory. The default is 4, which implies that the edge cache requires one byte of memory for each edge.

--paired-ends : The input read pairs are in paired-end format: L -> <- R. This is the default.

--mate-pairs : The read pairs are in mate-pair format: R <- -> L.

--innies : The read pairs are in 'innie' format: L -> <- R. This is the same as --paired-ends.

--outies : The read pairs are in 'outie' format: L <- -> R.

--delete-scaffold : By default, build-supergraph will not proceed if there are unapplied scaffold files from a previous run of build-scaffold present, e.g. because the scaffold command has not been run. This flag causes it to instead delete those files and continue.

goss thread-reads

goss thread-reads -G PREFIX {-I FASTA-filename | -i FASTQ-filename | --line-in filename}+ --expected-coverage INT [--min-link-count INT] [--edge-cache-rate INT]

The thread-reads command takes each individual read from the given input, and identifies the sequence of superpath segments that read runs through. Any pair of segments which is unambiguously linked by a sufficient number of reads, is then joined into a new, longer segment. Two segments are considered to be linked unambiguously if every read going through the first also runs through the second.

OPTIONS

-G PREFIX, --graph-in PREFIX : The name of the input graph. This is the string used as the prefix for the names of the files making up a graph object.

-I FILE, --fasta-in FILE : Input file in FASTA format.

-i FILE, --fastq-in FILE : Input file in FASTQ format.

--line-in FILE : Input file with one read per line and no other annotation.

--expected-coverate INT : The expected genome coverage of the reads used to build the underlying de Bruijn graph. These may or may not be the same as the read pairs used in this stage. This flag is mandatory.

--min-link-count INT : Disregard pairs of contigs which are linked by fewer than this number of reads. The default value is 10.

--edge-cache-rate INT : To efficiently locate reads within the supergraph, goss builds a data structure for caching the positions of de Bruijn graph edge within the supergraph edges that contain them. In order to save memory, this information is stored for only a proportion of the complete set of de Bruijn graph edges. For a value of n, position information is stored for one edge out of every 2^n, where each entry takes 16 bytes. High values will reduce memory usage, at the expense of an increased runtime, while lower values will lower the runtime, but require more memory. The default is 4, which implies that the edge cache requires one byte of memory for each edge.

--delete-scaffold : By default, build-supergraph will not proceed if there are unapplied scaffold files from a previous run of build-scaffold present, e.g. because the scaffold command has not been run. This flag causes it to instead delete those files and continue.

goss build-scaffold

goss build-scaffold -G PREFIX {-I FASTA-filename | -i FASTQ-filename | --line-in filename}+ --expected-coverage INT --insert-expected-size INT [--insert-size-std-dev FLOAT] [--insert-size-tolerance FLOAT] [--min-link-count INT] [--edge-cache-rate INT] [--paired-ends] [--mate-pairs] [--innies] [--outies]

DESCRIPTION

The build-scaffold command aligns pairs of reads to contigs in the supergraph and records the results alongside the graph for later use by the 'scaffold' command. If run multiple times, before invoking the 'scaffold' command, the pair aligment information is combined and will be applied by the 'scaffold' command at the same time. This is necessary to apply pairs from multiple insert libraries at the same time. (Different libraries can be applied separately by running 'build-scaffold' followed immediately by 'scaffold' for each library.)