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!!!
2 answers
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.
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.
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