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boss-fqsp.md

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Document for FQSP

Table of Contents

Aim

boss-fqsp is used to split one fastq file into two fastq files. The format of the input fastq file is as follows:

@SRR8618317.1.1 1 length=101
CAGTGCTCAGCTTGCACCCTGGCACAGGCCAGCAGTTGCTGGAAGTCAGACACCCGGTGCTGGCAATCTCGTTTAAACTACATGCAGGAACAGCAAAGGAA
+SRR8618317.1.1 1 length=101
?????????????????????????????????????????????????????????????????????????????????????????????????????
@SRR8618317.1.2 1 length=101
CCGGTGTTGAGAATGACTGCGCAAATTTGCCGGATTTCCTTTGCTGTTCCTGCATGTAGTTTAAACGAGATTGCCAGCACCGGGTGTCTGACTTCCAGCAA
+SRR8618317.1.2 1 length=101
?????????????????????????????????????????????????????????????????????????????????????????????????????

Every four lines are belong to one end of paired reads.

Usage

boss-fqsp -h will show the help message.

$ boss-fqsp -h
fqsp - A program to split ncbi fq files into forward and reverse files.
Usage:
  boss-fqsp [OPTION...] [input.fq|.fq.gz]

  -h, --help        Show help
  -v, --version     Print the current version number
  -o, --output arg  Output fq file
  -d, --debug       Enable debug mode
  • Example 1

The result example.1.fq and example.2.fq will be written.

$ boss-fqsp example.fq
  • Example 2

The result example.1.fq.gz and example.2.fq.gz will be written.

$ boss-fqsp example.fq.gz

Performance

The performance is tested simply by time command. It is not a benchmark. The slowest part is the gzip decompression and compression.

File Size Line Number Format Time
2.2G 420'010'288 fq.gz 18m
28G 420'010'288 fq 4m14s

Current Issues