https://github.com/arendsee/zwc

A fast version of the EMBOSS wordcount utility
https://github.com/arendsee/zwc

bioinformatics fasta wordcount

Last synced: 4 months ago
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A fast version of the EMBOSS wordcount utility

• Host: GitHub
• URL: https://github.com/arendsee/zwc
• Owner: arendsee
• License: other
• Created: 2014-10-20T05:02:43.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2018-12-11T04:22:30.000Z (over 7 years ago)
• Last Synced: 2024-06-11T16:26:39.393Z (almost 2 years ago)
• Topics: bioinformatics, fasta, wordcount
• Language: C++
• Size: 278 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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zwc

===

I wrote this program because I needed a fast fasta word counter and the EMBOSS ```wordcount``` utility is extremely slow.

zwc is on the order of 10X to 100X faster than EMBOSS' program, depending on the parameters and input data.

Installation

============

Install from github with

```R

library(devtools)

install_github('arendsee/zwc')

```

Usage

=====

```R

# Get counts of all 2-mers in a fasta file

fasta_wc("my-fasta-file.fa", k=2)

```