Source: python-sqt Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Section: science Testsuite: autopkgtest-pkg-python Priority: optional Build-Depends: debhelper (>= 12~), dh-python, python3-all, python3-dev, python3-setuptools, cython3, # Testing python3-nose, python3-cutadapt, python3-pysam, python3-seaborn, python3-xopen Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/python-sqt Vcs-Git: https://salsa.debian.org/med-team/python-sqt.git Homepage: https://bitbucket.org/marcelm/sqt Package: python3-sqt Architecture: any Section: python Depends: ${shlibs:Depends}, ${python3:Depends}, ${misc:Depends}, python3-seaborn, python3-matplotlib, python3-pysam (>= 0.10), python3-cutadapt Recommends: fonts-noto-color-emoji Description: SeQuencing Tools for biological DNA/RNA high-throughput data sqt is a collection of command-line tools for working with high-throughput sequencing data. Conceptionally not fixed to use any particular language, many sqt subcommands are currently implemented in Python. For them, a Python package is available with functions for reading and writing FASTA/FASTQ files, computing alignments, quality trimming, etc. . The following tools are offered: * sqt-coverage -- Compute per-reference statistics such as coverage and GC content * sqt-fastqmod -- FASTQ modifications: shorten, subset, reverse complement, quality trimming. * sqt-fastastats -- Compute N50, min/max length, GC content etc. of a FASTA file * sqt-qualityguess -- Guess quality encoding of one or more FASTA files. * sqt-globalalign -- Compute a global or semiglobal alignment of two strings. * sqt-chars -- Count length of the first word given on the command line. * sqt-sam-cscq -- Add the CS and CQ tags to a SAM file with colorspace reads. * sqt-fastamutate -- Add substitutions and indels to sequences in a FASTA file. * sqt-fastaextract -- Efficiently extract one or more regions from an indexed FASTA file. * sqt-translate -- Replace characters in FASTA files (like the 'tr' command). * sqt-sam-fixn -- Replace all non-ACGT characters within reads in a SAM file. * sqt-sam-insertsize -- Mean and standard deviation of paired-end insert sizes. * sqt-sam-set-op -- Set operations (union, intersection, ...) on SAM/BAM files. * sqt-bam-eof -- Check for the End-Of-File marker in compressed BAM files. * sqt-checkfastqpe -- Check whether two FASTQ files contain correctly paired paired-end data.