FqKit -- A simple and cross-platform programfor fastq file manipulationVersion: 0.4.12Authors: sharkLoc<mmtinfo@163.com>Source code: https://github.com/sharkLoc/fqkit.gitFqkit supports reading and writing gzip (.gz) format.Bzip2 (.bz2) format is supported since v0.3.8.Xz (.xz) format is supported since v0.3.9.Under the same compression level, xz has the highest compression ratio but consumes more time. Compression level: format range default crate gzip 1-9 6 https://crates.io/crates/flate2 bzip2 1-9 6 https://crates.io/crates/bzip2 xz 1-9 6 https://crates.io/crates/xz2Usage: fqkit [OPTIONS]<COMMAND>Commands: topn get first N records from fastq file [aliases: head] tail get last N records from fastq file concat concat fastq files from different lanes subfq subsample sequences from big fastq file [aliases: sample]selectselect pair-end reads byread id trim trim fastq reads by position adapter cut the adapter sequence on the reads filter a simple filterfor pair end fastq sqeuence join join paired end reads that are overlapping into a single longerread range print fastq recordsin a range search search reads/motifs from fastq file grep grep fastq sequence byread id or full name stats summaryfor fastq format file [aliases: stat] kmer a simple kmer counter shuffle shuffle fastq sequences size report the number sequences and bases slide extract subsequencesin sliding windows sort sort fastq file by name/seq/gc/length plot line plotforA T G C N percentageinread position fq2fa translate fastq to fasta fq2sam converts a fastq file to an unaligned SAM file fqscore converts the fastq file quality scores flatten flatten fastq sequences [aliases: flat] barcode perform demultiplexfor pair-end fastq reads [aliases: demux] check check the validity of a fastq record remove remove reads byread name rename rename sequence idin fastq file reverse get a reverse-complement of fastq file [aliases: rev] split split interleaved fastq file merge merge PE reads as interleaved fastq file mask convert any low quality base to'N' or other chars split2 split fastq file by records number gcplot get GC content result and plot length get reads length count [aliases: len] view view fastq file page by pagehelp Print this message or thehelp of the given subcommand(s)Global Arguments: -@, --threads<INT> threads number [default: 4] --compress-level<INT>set gzip/bzip2/xz compression level 1 (compress faster) - 9 (compress better)for gzip/bzip2/xz output file, just work with option -o/--out [default: 6] --output-type<u|g|b|x> outputtypefor stdout:'g' gzip;'b' bzip2;'x' xz;'u' uncompressed txt format [default: u --log<FILE>if file name specified, write log message to this file, or write to stderr -v, --verbosity... control verbosity of logging, [-v: Error, -vv: Warn, -vvv: Info, -vvvv: Debug, -vvvvv: Trace, defalut: Debug]Global FLAGS: -q, --quiet be quiet anddo not show any extra information -h, --help printshelp information -V, --version prints version informationUse"fqkit help [command]"for more information about acommand
