This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Finding Common Reads Across Multiple Fastq Files

Hi All

We have some metagenome samples(multiple illumina lanes). What I would like to do is find out % of reads that are common amongst these fastq's allowing upto #N mismatches.

I think I can take a subsample of the reads from each fastq/bin and compare them but just wondering if there is a slick approach to do the comparison.

Thanks! -Abhi

fastq
• 4,957 views • link
updated by Manu Prestat Manu Prestat • written by Abhi Abhi

Do you allow difference of quality?

• 0 views • link
written by Manu Prestat Manu Prestat

@Manu : For now I dint think about it. I was just wondering if we can comapre the reads at base level and allowing 2-4 mismatches between the reads should cover for difference in quality scores.

• 0 views • link
written by Abhi Abhi

2 answers

I'd start by looking at the tools contained in vmatch. There are probably many ways to approach this problem but it seems sensible to use some kind of indexing on the fastq files prior to doing the comparisons.

• 0 views • link
written by Mikael Huss Mikael Huss

neat software, did not about it before

• 0 views • link
written by Istvan Albert Istvan Albert

cd-hit would do what you want. I just learnt by the way that you can directly use fastq file as input. You can also take a look at uclust (usearch).

• 1 views • link
written by Manu Prestat Manu Prestat

Log in to answer this question.

More posts like this