fqkit

namefqkit
created_at2022-12-06 08:24:46.225215
updated_at2023-12-21 06:39:00.488027
downloads1212
descriptionfqkit: a simple and cross-platform program for fastq file manipulation
homepagehttps://github.com/sharkLoc/fqkit
repository
max_upload_size
id730994
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documentation

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![icon](https://github.com/sharkLoc/fqkit/blob/main/doc/fqkit_icon.PNG) # fqkit ![Static Badge](https://img.shields.io/badge/Author-sharkLoc-blue) ![Static Badge](https://img.shields.io/badge/Tool-fqkit-red) ![Crates.io (latest)](https://img.shields.io/crates/dv/fqkit?labelColor=rgb&color=hex&link=https%3A%2F%2Fcrates.io%2Fcrates%2Ffqkit) ![Crates.io](https://img.shields.io/crates/d/fqkit?label=Total%20download%20in%20crate.io) ![GitHub Gist last commit](https://img.shields.io/github/gist/last-commit/a4910923a230b8975218a188528463d7?logo=github) 🦀 a simple program for fastq file manipulation ## install ##### setp1: install cargo first ```bash curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh ``` ##### step2: on linux or windows ```bash cargo install fqkit # or git clone https://github.com/sharkLoc/fqkit.git cd fqkit cargo b --release # mv target/release/fqkit to anywhere you want ``` ## usage ```bash FqKit -- A simple and cross-platform program for fastq file manipulation Version: 0.3.6 Authors: sharkLoc Source code: https://github.com/sharkLoc/fqkit.git Usage: fqkit.exe [OPTIONS] Commands: topn get first N records from fastq file concat concat fastq files from different lanes subfq subsample sequences from big fastq file [aliases: sample] trim trim fastq file filter a simple filter for pair end fastq sqeuence range print fastq records in a range search search reads/motifs from fastq file grep grep fastq sequence by read id or full name stats summary for fastq format file [aliases: stat] shuffle shuffle fastq sequences size report the number sequences and bases slide extract subsequences in sliding windows sort sort fastq file by name/seq/gc/length plot line plot for A T G C N percentage in read 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 join join paired end reads that are overlapping into a single longer read barcode split barcode for PE reads check check the validity of a fastq record remove remove reads by read name 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 view view fastq file page by page help Print this message or the help of the given subcommand(s) Options: -h, --help Print help -V, --version Print version Global Arguments: --compress-level set gzip compression level 1 (compress faster) - 9 (compress better) for gzip output file, just work with option -o/--out [default: 6] --log if file name specified, write log message to this file, or write to stderr -v, --verbosity control verbosity of logging, possible values: {error,warn,info,debug,trace} [default: debug] Global FLAGS: -q, --quiet be quiet and do not show any extra information Use "fqkit help [command]" for more information about a command ``` ## change log
timeline 2023.11.03: - update to version 0.2.12 - add subcommand trim - update cmd help information 2023.11.08: - update to version 0.2.13 - add subcommand reverse 2023.11.10: - update to version 0.2.14 - add subcommand view - rebuilt some command interface 2023.11.29: - update to version 0.2.15 - recode func in stats subcommand 2023.12.04 - update to version 0.2.16 - add subcommand size 2023.12.05 - update to version 0.2.17 - update code for subcommand size and search - add subcommand fq2sam - add log information options verbosity 2023.12.09 - update to version 0.2.18 - add subcommand sort, range, check and mask - update to version 0.2.19 - add subcommand shuffle 2023.12.10 - update to version 0.3.0 - add glob option --compress-level for gzip output file 2023.12.11 - update to version 0.3.1 - add subcommand grep and fqscore 2023.12.11 - update to version 0.3.2 - add subcommand slide 2023.12.19 - update to version 0.3.5 - add subcommand filter
#### ** any bugs please report issues **💖
Commit count: 0

cargo fmt