polishgenomejs

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.

Install

npm install polishgenomejs --save

Use

  const polish = require('polishgenomejs')
  const fastq = "header (not used)\nACAAG\n'1!!1\n"
  console.log(polish(fastq))

Options:

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).

Step

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.

Example

polish(data, { minLength: 10, minQuality: !, searchLength: 5 }, 4)

Git

https://www.github.com/zpeterg/polishgenomejs