FastProNGS

　This tool is designed to preprocess fastq files, it can fast cut adapter, QC, trimming, statistics 　from raw data by all-in-one or step by step. it is developed in c with multithreading supported to 　be afford high performance.

Install

　download binary (https://github.com/Megagenomics/FastProNGS/)

　make

　make install

Dependencies

　libxml2

Usage

　Usage: FastProNGS [-agbAGBieOqQlnrmMcEopsxHTjRtwh?v] [file ...]
　-a --adapter The 3' end adapter (if paired data, represent first read). Supporting anchoring '$'.
　-g --front The 5' end adapter (if paired data, represent first read). Supporting anchoring '^'.
　-b --anywhere The 3' or 5' end adapter (if paired data, represent first read).
　-A --adapter2 The 3' end adapter (if paired data, represent second read). Supporting anchoring '$'.
　-G --front2 The 5' end adapter (if paired data, represent second read). Supporting anchoring '^'.
　-B --anywhere2 The 3' or 5' end adapter (if paired data, represent second read).
　-i --no-indels Allow only mismatches in alignments, (Default: allow both mismatches and indels).
　-e --error-rate Maximum allowed error rate (no. of errors divided by the length of the matching region. Default: see xml).
　-O --overlap Require MINLENGTH overlap between read and adapter for an adapter to be found, (Default: see xml).
　-q --quality-filter Discard reads when it less than specific threshold or ratio. (Format:threshold,ratio).
　-Q --quality-low Cut base less than specific value in anywhere end.
　-n --trim-n Trim N's on ends of reads (Default: see xml).
　-r --ratio-n Discard reads greater than ratio-n (Default: see xml).
　-m --min-length Discard reads shorter than LENGTH (Default: see xml).
　-M --max-length Discard reads longer than LENGTH (Default: see xml).
　-c --gc-content Discard reads less than specific value (Default: see xml).
　-E --quality-base quality base (Default: see xml).
　-o --output1 Write trimmed reads1 to FILE.
　-p --output2 Write trimmed reads2 to FILE.
　-s --split split file count.
　-x --xml Default configuration file path

　-H --html html report file.
　-T --text text report file.
　-j --json json report file.
　-R --title title of report
　-t --threads threads of program.
　-k --reads the num of request read
　-h --help print help message.
　-v --version print version message.

Author

　BT team, 1 March 2018, http://www.megagenomics.cn/