python3-sqt binary package in Ubuntu Lunar amd64
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.
Publishing history
Date | Status | Target | Component | Section | Priority | Phased updates | Version | ||
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2023-03-15 13:39:18 UTC | Published | Ubuntu Lunar amd64 | release | universe | python | Optional | 0.8.0-6build1 | ||
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Deleted | Ubuntu Lunar amd64 | proposed | universe | python | Optional | 0.8.0-6build1 | |||
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2023-03-15 13:39:24 UTC | Superseded | Ubuntu Lunar amd64 | release | universe | python | Optional | 0.8.0-6 | ||
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2023-03-16 18:10:12 UTC | Deleted | Ubuntu Lunar amd64 | proposed | universe | python | Optional | 0.8.0-6 | ||
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2022-12-04 09:14:18 UTC | Superseded | Ubuntu Lunar amd64 | release | universe | python | Optional | 0.8.0-5build2 | ||
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2022-12-05 12:10:12 UTC | Deleted | Ubuntu Lunar amd64 | proposed | universe | python | Optional | 0.8.0-5build2 | ||
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2022-11-04 01:09:19 UTC | Superseded | Ubuntu Lunar amd64 | release | universe | python | Optional | 0.8.0-5build1 | ||
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