Biostar Test Site

This is site is used for testing only. Visit: https://www.biostars.org to ask a question.

vg paired end short read mapping: Best practice?
1
1
Entering edit mode
9 months ago

I'm trying to map short reads to a genome graph constructed from multiple whole genome alignments of A. thaliana. What is the best practice method to produce the alignments in a reasonable time frame. I've been mapping just a subset of 5000 pairs to a single chromosome graph. vg map takes >24h to complete and enormous resources (up to 500G of RAM on a single core). Mapping a full sequencig run to the full genome graph took over 7 days to complete. Any help would be appreciated. Thanks!!!

mapping short read genome graph vg • 356 views
ADD COMMENT
0
Entering edit mode
9 months ago
xwwang ▴ 20

In my experience, you can use the multiple threads to speed up via the -t option: -t $nthread

where $nthread is the number of threads, e.g. 10

In this way, it will be much fast. It took me one day for 200 million paired-end reads to map to a large graph.

ADD COMMENT

Login before adding your answer.

Traffic: 196 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6