NAME

       sqt - SeQuencing Tools for biological DNA/RNA high-throughput data

DESCRIPTION

       usage: sqt [-h] [--version]

              {align,  bam2fastq,  fastxmod,  qgramfreq,  chars,  fastagrep,  readcov, randomseq,
              samsetop, bameof, readlenhisto, cutvect} ...

       SeQuencing Tools -- command-line tools for working with sequencing data

   positional arguments:
              {align, bam2fastq,  fastxmod,  qgramfreq,  chars,  fastagrep,  readcov,  randomseq,
              samsetop, bameof, readlenhisto, cutvect}

       align  Compare two strings

       bam2fastq
              Extract all reads from a BAM file that map to a certain location, but try hard

       fastxmod
              Modify FASTA and FASTQ files by picking subsets and modifying individual entries.

       qgramfreq
              Print q-gram (also called k-mer) frequencies in a FASTA or FASTQ file.

       chars  Print the number of characters in a string.

       fastagrep
              Search for a IUPAC string in the sequences of a FASTA file.

       readcov
              Print a report for individual reads in a SAM/BAM file.

       randomseq
              Generate random sequences in FASTA format

       samsetop
              Perform set operation on two SAM/BAM files.

       bameof Check whether the EOF marker is present in BAM files.

       readlenhisto
              Print and optionally plot a read length histogram of one or more FASTA or FASTQ

       cutvect
              Remove vector sequence

   optional arguments:
       -h, --help
              show this help message and exit

       --version
              show program's version number and exit

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.