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.

sqt 0.8.0                                         January 2019                                            SQT(1)