SeQuencing Tools for biological DNA/RNA high-throughput data
Descriptionsqt 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
* sqt-fastaextract -- Efficiently extract one or more regions from an
indexed FASTA file.
* sqt-translate -- Replace characters in FASTA files (like the 'tr'
* sqt-sam-fixn -- Replace all non-ACGT characters within reads in a
* sqt-sam-insertsize -- Mean and standard deviation of paired-end
* sqt-sam-set-op -- Set operations (union, intersection, ...) on
* sqt-bam-eof -- Check for the End-Of-File marker in compressed
* sqt-checkfastqpe -- Check whether two FASTQ files contain correctly
paired paired-end data.
Upload more screenshots
Please help extend the collection of screenshots. Just make a screenshot and upload it here. You don't need to register or anything.Upload a screenshot
Hint: upload an image here from your clipboard with Ctrl-V
Install this software package
If the package is available for the distribution you are currently using on your computer then install the software by clicking on…Install python3-sqt