biTK package

Prerequisites

1. Jinja2
2. Matplotlib

Download and Installation

pysetup run build install_dist --prefix=/path/to/install or python setup.py install

Command Line Options

python -m 'biTK.ngs.apps.statsApp'

Usage: statsApp.py [optioins] --fastq xx.fastq

Options: --version show program's version number and exit -h, --help show this help message and exit

General options: --action=ACTION The input file in fastq format[REQUIRED]. --fastqfile=FASTQFILE The input file in fastq format[REQUIRED]. -o OUTFILE, --out=OUTFILE The output file after trimming sequences. --reportfile=REPORTFILE The output path of html report file. --quality-score-fmt=QUALITY_SCORE_FMT The format of quality scores used in fastq format. --log=LOGFILENAME The name of a log file. If not specified, the name will be biTK.log -v, --verbose Show verbose info

Trimming options: --trim-minlen=TRIM_MIN_LEN Remove sequences that are shorter than minimum length --trim-inplace Triming sequences inplace without making a duplicate data --trim-qs-cutoff=TRIM_QUALITY_SCORE_CUTOFF Trim n bases in the head of a sequence, default is 30. --trim-len-head=TRIM_LEN_HEAD Trim n bases in the head of a sequence, default is 10. --trim-len-tail=TRIM_LEN_TAIL Trim n bases in the tail of a sequence, default is 10. --trim-quality-head=TRIM_QUALITY_HEAD Trim bases with quality score of less than threshold in the head of a sequence --trim-quality-tail=TRIM_QUALITY_TAIL Trim bases with quality score of less than threshold in the tail of a sequence. -a TRIM_ADAPTER, --trim_adapter=TRIM_ADAPTER Trim an adapter sequence.

Statistics options: Option arguments for statistics.

-k STATS_KMER, --kmer=STATS_KMER
                    Occurrencies of k-mer continuous bases
-n STATS_NHEAD, --nhead=STATS_NHEAD
                    Occurrencies of k-mer continuous bases