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All Projects → lh3 → calN50

lh3 / calN50

Licence: other
Compute N50/NG50 and auN/auNG

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javascript
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bioinformaticsgenomics

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Getting Started

## If you can run paftools.js from minimap2, you already have k8 installed. If not:

## install k8 without conda:
# curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
# cp k8-0.2.4/k8-`uname -s` k8         # or copy it to a directory on your $PATH

## install k8 via bioconda:
# conda install -c bioconda minimap2   # k8 comes with minimap2

k8 calN50.js ctg.fa             # compute auN and N50 from FASTA
./calN50.js ctg.fa.fai          # faidx index (assuming k8 on $PATH)
calN50.js graph.gfa.gz          # if k8 and calN50.js are on $PATH
calN50.js -L3.1g ctg.fa.fai     # compute auNG and NG50 for a 3.1Gbp genome
calN50.js -f ref.fa.fai ctg.fa  # or get the genome size from a .fai file

Introduction

calN50.js is a simple script to calculate N50/NG50 and auN/auNG. It is fast and seamlessly works with FASTA, GFA1 and faidx formats.

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