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.
download binary (https://github.com/Megagenomics/FastProNGS/)
make
make install
libxml2
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.
BT team, 1 March 2018, http://www.megagenomics.cn/