v0.10.3

Install piscem 0.10.3

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.10.3/piscem-installer.sh | sh

Download piscem 0.10.3

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

v0.10.2

Install piscem 0.10.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.10.2/piscem-installer.sh | sh

Download piscem 0.10.2

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

v0.10.1

Install piscem 0.10.1

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.10.1/piscem-installer.sh | sh

Download piscem 0.10.1

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

v0.10.0

Bug fixes:

• Fixes bug where reads were not parsed properly in custom chemistry in which the mappable (biological) sequence spanned more than one read. If one had encountered this bug it would almost certainly be obvious, as you'd likely have seen no mapped reads.

• Fixes bug in paired-end mapping in bulk-mode piscem, when using the poison table, where reads might have wrongly been reported as aligned when they should have been poisoned. This has been fixed and was never present in single-cell-mode, as this is the first release to support biological paired-end single-cell data.

New Features:

• Support for taking advantage of biological paired-end read information, in single-cell data, in protocols supporting this. It is now possible to have "mappable" portions of both read 1 and read 2. These are treated as normal paired-end reads. Currently, for downstream processing of the RAD files, the entire fragment is assigned an orientation (i.e. the orientation of the individual reads are not recorded separately in the RAD file). The current behavior is that for single-end data, the orientation of the mapped read is recorded and for paired-end data, the orientation of the first read in the pair, i.e. read 1, (either observed or implied) is recorded. For example, if a read pair maps with read 1 in the forward orientation and read 2 in the reverse complement orientation, this is recorded as a forward read. Likewise, if read 1 doesn't map but read 2 maps in the reverse complement orientation, this is also considered as a forward read, as reads in paired-end protocols are expected to map in opposite orientations. On the other hand, if the geometry is single-end, and read 2 is the biological read, then the orientation will be recorded as reverse complement if read 2 maps in the reverse complement orientation.

• Explicit flags for chromium_v2_5p, chromium_v3_5p and chromium_v4_3p, corresponding to 10x Chromium v2 and v3 5' chemistries and Chromium v4 3' chemistry respectively.

  • The chromium_v4_3p flag is a convenience, as the geometry is identical to chromium_v3 (though the associated permit list is different), however the distinct flag better conveys intent.

  • The 5' chemistries are treated as biological paired-end protocols by default; that is, if read 1 is long enough to have mappable sequence (i.e. if the length of the read is longer than the barcode length + UMI length + TSO length + k-1, where k is the length of the k-mers used in the piscem index), then that sequence is mapped. However, if read 1 only contains technical information (e.g. UMI and barcode), then just read 2 is mapped. Note however, that treating 5' chemistry as paired-end has implications on the implied orientation reported in the RAD file (see above).

Install piscem 0.10.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.10.0/piscem-installer.sh | sh

Download piscem 0.10.0

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

v0.9.0

Note : piscem v0.9.0 was incorrectly tagged, and is functionally near equivalent to v0.8.0. Please upgrade to piscem v0.10.0.

Install piscem 0.9.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.9.0/piscem-installer.sh | sh

Download piscem 0.9.0

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

v0.8.0

Install piscem 0.8.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.8.0/piscem-installer.sh | sh

Download piscem 0.8.0

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

v0.7.3

Install piscem 0.7.3

Changes

• Changed the default working directory for files created during index construction
  • This was previously the current directory . and has been made .workdir.noindex. This was done to avoid the temporary creation of many files in the current directory, which could be messy if the execution was terminated early. The .noindex extension is geared at preventing Spotlight from indexing this folder by default on OSX.
• Moved to the cloudflare-based zlib implementation, rather than standard zlib by default in piscem-cpp.
• Added default values for the k-mer (31) and minimizer (19) lengths.
• Grouped many command line parameters under help headings to better organize the output of the --help flag.
• Added better parameter validation for the k-mer length (must be <= 31 and odd).
• Updated crate dependencies, and upgraded cargo-dist version to 0.10.0.

Special thanks to @ialbert for noticing the poor interaction between the cuttlefish temporary files and spotlight and for suggesting placing these in a subdirectory by default, and also for suggesting adopting defaults for the k-mer and minimizer lengths.

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.7.3/piscem-installer.sh | sh

Download piscem 0.7.3

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

v0.7.2

Install piscem 0.7.2

From the perspective of functionality, this release is identical to piscem 0.7.1. The main purpose of this release is to introduce the auto-generated cargo dist-powered builds. This should make it easy to automatically create and release pre-compiled binaries for major platforms using GitHub runners. Below, you'll find binaries for Apple silicon, OSX (x86_64), and linux (x86_64). You can also install piscem directly into your cargo binary directory using the shell script command below.

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.7.2/piscem-installer.sh | sh

Download piscem 0.7.2

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum

piscem v0.7.1

This release adds the ability to (optionally) provide a seed parameter for SSHash construction. In rare situations, SSHash construction can fail due to empty buckets in the skew index (this is a technical detail you need not be concerned with as a user). Usually, this issue can be resolved by just attempting to build the index again with a different seed. The --seed option to piscem build will allow you to set the seed used in construction (the default seed is 1).

Piscem v0.7.0

This release of piscem adds the ability to index decoy sequencing using the "distinguishing flanking k-mer" methodology described in Hjörleifsson and Sullivan et al.¹. This variant of considering decoy sequences that is optimized to work with pseudoalignment and pseudoalignment-like approaches where alignment scores are unavailable (unlike the approach of ², which is designed to work with selective-alignment).

The implementation in piscem adopts the terminology of "poison" k-mers — that is, the decoy sequence is used to create a separate table of poison k-mers whose presence will cause a read to be discarded, rather than to map to some target in the index. Poison k-mers are simply distinguishing flanking k-mers that belong to some decoy sequence, and hence their presence in a mapping should "poison" the mapping (i.e. lead to it being discarded).

To build a decoy-aware index, one simply passes the --decoy-paths argument to piscem build. This accepts a , separated list of FASTA files that will be used to generate the poison k-mer set. This will create a separate data structure (the poison table) that will be used to filter fragments that are potentially mapped spuriously to the index.

Likewise, when performing mapping, if a poison table has been built, it will be used by default. However, you can pass the --no-poison flag to map-bulk and map-sc to avoid considering poison k-mers, even if the index was constructed with a poison table.

1. Eldjárn Hjörleifsson, Kristján, et al. "Accurate quantification of single-nucleus and single-cell RNA-seq transcripts." bioRxiv (2022): 2022-12. ↩

2. Srivastava, Avi, et al. "Alignment and mapping methodology influence transcript abundance estimation." Genome biology 21.1 (2020): 1-29. ↩