README.md

What is seqproc?

seqproc is a program for interpreting and transforming sequencing data according to the extended fragment geometry description language (EFGDL). In fact, the seqproc executable is a rather thin wrapper around the underlying seqproc library, whose main purpose is to accept an input stream of reads (consisting of single-end or paired-end reads) and an EFGDL specification, and to transform the input reads into the desired output formation according to the specification.

Thus the important information regarding seqproc actually pertains to the EFGDL, which has its own documentation. For detailed documentation describing EFDGL, please visit the EFGDL specification documentation here

Using seqproc

The seqproc program is an executable that exposes a single command that takes several command line arguments. You can pass the -h or --help flag to seqproc to see the various command line arguments and their descriptions.

$ ./target/release/seqproc -h
General puprose sequence preprocessor

Usage: seqproc [OPTIONS] --geom <GEOM> --file1 <FILE1> --file2 <FILE2>

Options:
  -g, --geom <GEOM>                 EFGDL string
  -1, --file1 <FILE1>               r1 fastq file
  -2, --file2 <FILE2>               r2 fastq file
  -o, --out1 <OUT1>                 r1 out fastq file [default: ]
  -w, --out2 <OUT2>                 r2 out fastq file [default: ]
  -t, --threads <THREADS>           number of threads to use [default: 1]
  -a, --additional <ADDITIONAL>...
  -h, --help                        Print help