A simple tool for aligning and polishing genomes in JavaScript. This is only a prototype at this point. It provides only basic length/quality screen and sligns by string.
npm install polishgenomejs --save
const polish = require('polishgenomejs')
const fastq = "header (not used)\nACAAG\n'1!!1\n"
console.log(polish(fastq))
The 2nd optional argument.
minLength: int(default 10): Minimum length-per-sequence.
minQuality: int(0-94, default 10): Minimum quality-per-nucleotide.
searchLength: int(default 5): Length of nucleotide string used to find a match (does not yet accommodate errors, so should be fairly short).
The 3rd optional argument - the step to stop at. Defaults to all steps (4 or more). Step 1: Only filter by length. Step 2: Filter by length and quality. Step 3: Above + Align columns. Step 4: Above + add Consensus column.
polish(data, { minLength: 10, minQuality: !, searchLength: 5 }, 4)
https://www.github.com/zpeterg/polishgenomejs