pairgen
paired-end NGS simulator
Overview
Installation
npm install pairgen
Usage
command line
$ pairgen [options] <fasta file> [<ranges bed file>]
[options]
--name name of the sequence. default = basename(path)
--readlen length of the read. default = 100
--tlen length of the template. default = 400
--dev standard deviation of the total fragment length. default = 50
--depth physical read depth. default = 40
--save_dir directory to save result. default = /home/shinout/node_modules/pairgen
--pair_id <id_type> pair id type, put pair information explicitly. id_type is one of A, 1, F, F3.
--parallel the number of processes to run. default: 1
--p5 Illumina P5 adapter. default: GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
--p7 Illumina P7 adapter. default: ACACTCTTTCCCTACACGACGCTCTTCCGATCT
--adapter1 Illumina Sequence Primer#1. default: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
--adapter2 Illumina Sequence Primer#2. default: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT