fastq barcode split

双端测序数据barcode拆分工具

• 目前只支持单barcode拆分
• 支持gz压缩文件输入输入
• 参数支持barcode碱基容错
• 支持一个样本对应多个barcode

repo :

github : https://github.com/sharkLoc/fqkit.git

install :

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 :

fqkit barcode --help
split barcode for PE reads

Usage: fqkit barcode [OPTIONS] --read1 <READ1> --read2 <READ2> --barcode <BAR>

Options:
  -1, --read1 <READ1>     input read1 fastq[.gz] file
  -2, --read2 <READ2>     input read2 fastq[.gz] file, barcode in this file
  -b, --barcode <BAR>     barcode list file, format eg:
                          ATGCAGTG    sample1
                          TGCAGTAC    sample2
  -m, --mode <MODE>       barcode position mode, 1:left, 2:right [default: 2]
  -r, --rev_comp          barcode reverse complement
  -e, --error <MISMATCH>  barcode mismatch base count [default: 0]
  -o, --outdir <OUTDIR>   fastq file output dir [default: .]
  -h, --help              Print help information