fastqparser

README

fastqparser is a Fastq stream parser

Usage

Parse a fastq.gz filestream. Omit the zlib pipe if the file is uncompressed.

var zlib = require('zlib');
var fs = require('fs');
var fastq = require('fastq'); // require('./index');

fs.createReadStream('path/to/example.fastq.gz')
	.pipe(zlib.createUnzip())
	.pipe(fastq.obj())
	.pipe(do_something())
	.on('finish', function(){
		console.log("Done");
	});

Parse a fastq.gz S3 object

var s3 = require('aws-sdk/clients/s3');
s3.getObject({bucket: 'bucketname', path: 'path/to/file.fastq.gz'}).createReadStream()
	.pipe(zlib.createUnzip())
	.pipe(fastq.obj())
	.pipe(do_something())
	.on('finish', function(){
		console.log("Done");
	});

Alternatives

I've been needing a streamable fastq file parser, and didn't like the development state of bionode-fastq, which implements a different file-only base API compared to the stellar bionode-fasta. My philosophy is similar to fastqstream.

• fasta-tools
• fqreader
• bionode-fastq
• streaming-sequence-extractor

License

GPL-3.0