[ 源代码： python-sqt ]
软件包：python3-sqt（0.8.0-3）
SeQuencing Tools for biological DNA/RNA high-throughput data
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.
其他与 python3-sqt 有关的软件包
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- dep: libc6 (>= 2.14) [amd64]
- GNU C 语言运行库：共享库
同时作为一个虚包由这些包填实： libc6-udeb
- dep: libc6 (>= 2.17) [arm64]
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- dep: python3
- 交互式高级面向对象语言（默认 python3 版本）
- dep: python3 (<< 3.8)
- dep: python3 (>= 3.7~)
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- dep: python3-cutadapt
- Clean biological sequences from high-throughput sequencing reads (Python 3)
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- dep: python3-matplotlib
- Python based plotting system in a style similar to Matlab (Python 3)
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- dep: python3-pysam (>= 0.10)
- interface for the SAM/BAM sequence alignment and mapping format (Python 3)
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- dep: python3-seaborn
- statistical visualization library for Python3
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- dep: python3-xopen
- Python3 module to open compressed files transparently
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- rec: fonts-noto-color-emoji
- color emoji font from Google