fastq

Commands under this group takes fastq files as input, compute read length distribution and plot them as interactive line plots.

parse-read-length

For a given fastq file, compute read lengths and write the distribution to json format

Options

option	description	required
–fastq	Fastq file (supports .gz files)	✓
–json	File name for json formatted output file	✓

Usage

ngs-statter parse-read-length --fastq path/to/fastq.gz --json path/to/output.json

plot-read-length

Given a list of json files containing read length distribution (generated using parse-read-length), plot the read length distribution as an interactive (html) line plot.

Options

option	description	required	default value
–json-dir	Directory containing json formatted read_length files (see parse-read-length). Either –json-dir or json formatted files as space separated arguments MUST be provided	✗
–html	Output file name	✓
–min-read-length	Minimum read length that will be kept	✗	15
–pattern	If –json-dir is provided, use this pattern to match files	✗	*.json
–title	Plot title	✗	Read length distribution after adapter trimming

Usage

using --json-dir

# using --json-dir
ngs-statter plot-read-length --json-dir path/to/json/dir --html path/to/output.html

using space separated json files as arguments

# using space separated json files as arguments
ngs-statter plot-read-length --html path/to/output.html path/to/fq1.json path/to/fq2.json