Question: Proper use of BWA-backtrack and BWA-MEM
gravatar for cfarmeri
3.9 years ago by
cfarmeri160 wrote:

Hi, Biostars.

I have a set of Illumina GA2 paired-end fastq files.

These reads of the fastqs has 76b length.

Before mapping, I trimmed barcode sequence from 5' end of both 1st and 2nd reads, finally, the reads have 63-67bp length.

BWA's author says following.

・reads < 70bp should be mapped by BWA-backtrack (BWA-backtrack can map 70bp< and <100bp reads, but they mention than these reads should be BWA-MEM algorithm.)

・reads > 100bp should be mapped by BWA-MEM. BWA-MEM algorithm is recommeded.

Any one has an idea which BWA-backtrack or BWA-MEM I should use?? Thanks!!!

genome • 3.3k views
ADD COMMENTlink modified 3.9 years ago by dariober11k • written 3.9 years ago by cfarmeri160
gravatar for Brian Bushnell
3.9 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

If the reads are < 70 bp after trimming, which it sounds like they are, then the official advice is to use BWA-backtrack. It does not matter how long they were initially.

Personally, if I were to use a BWA variant, I would choose BWA-mem over BWA-backtrack because it is so much faster and, in my testing, more accurate. But I have not tested it on < 70bp reads.

ADD COMMENTlink written 3.9 years ago by Brian Bushnell17k

Thanks, Brian.

I confused the 63-67bp is a value close to 70bp. First of all, I try BWA-backtrack algorithm.

ADD REPLYlink written 3.9 years ago by cfarmeri160
gravatar for dariober
3.9 years ago by
WCIP | Glasgow | UK
dariober11k wrote:

Hi- Have a look also at this post When and why is bwa aln better then bwa mem?

Personally, these days I use bwa mem even when read length is < 70bp. I haven't tested it properly, but I find that for shorter reads, especially if paired-end, bwa mem becomes slower and more memory hungry than bwa aln.

ADD COMMENTlink written 3.9 years ago by dariober11k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 930 users visited in the last hour