SciLifeLab/gapest

Name: gapest

Owner: Science For Life Laboratory

Description: Reference implementation of the scaffolding gap size estimation algorithm by Kristoffer Sahlin

Created: 2012-05-04 11:47:23.0

Updated: 2016-01-19 09:35:39.0

Pushed: 2013-04-02 08:56:22.0

Homepage: null

Size: 332

Language: Python

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README

GapEst

Reference implementation of the scaffolding gap size estimation algorithm by Kristoffer Sahlin.

Dependencies

Python modules scipy, pysam0.6, networkx1.4

INPUT

Required arguments:

1. -c a contig file (path to)

2. -f a BAM of SAM file (path to)

3. -m the mean of the insert sizes of the library (integer)

4. -s standard deviation of the library (integer)

5. -r (integer number) Mean read length for each of the libraries.

Optional:

1. -e (integer number, default 10) The least amount of witness links that is needed to create a link edge in graph to estimate gap for

Example run

python Main.py  -c /path/to/contigfile.fa -f /path/to/file1.bam /path/to/file2.bam -o /path/to/output -m <mean> -s <std dev>

Reference

http://bioinformatics.oxfordjournals.org/content/28/17/2215.long

The supplemental materials to the above paper is found as a PDF in the docs directory.