[bioinfo]fastqファイルを分割する

fastqファイルを分割するのはseqkitで下記のコマンドで行えるが、

seqkit split <fastq_file>

  -i, --by-id              split squences according to sequence ID
  -p, --by-part int        split sequences into N parts
  -r, --by-region string   split squences according to subsequence of given region. e.g 1:12 for first 12 bases, -12:-1 for last 12 bases. type "seqkit split -h" for more examples
  -s, --by-size int        split sequences into multi parts with N sequences
  -d, --dry-run            dry run, just print message and no files will be created.
  -f, --force              overwrite output directory
  -h, --help               help for split
  -k, --keep-temp          keep tempory FASTA and .fai file when using 2-pass mode
  -O, --out-dir string     output directory (default value is $infile.split)
  -2, --two-pass           two-pass mode read files twice to lower memory usage. (only for FASTA format) 

ファイルが大きすぎるとRAMが足りずに落ちる。その場合は、FASTQ Splitterを用いる。

Usage: fastq-splitter.pl [options] <file>...
Options:
     --n-parts    - Divide into  parts
     --part-size  - Divide into parts of size 
     --measure (all|seq|count) - Specify whether all data, sequence length, or
                            number of sequences is used for determining part
                            sizes ('all' by default).
     --eol (dos|mac|unix) - Choose end-of-line character ('unix' by default).
     --check              - Check FASTQ correctness.
     --version            - Show version.
     --help               - Show help.