python-sqt 0.8.0-5 source package in Ubuntu

 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.