Which aligners are commonly used for DNA-seq data alignment?

Question

[manojkumar_bhosale]

I want to know the aligners used commonly for DNA-seq data more specifically exome, amplicon data. I have used BWA-MEM and want to know about any other alternatives. Open source tools will be preferable.

Answer 1

[ATpoint]

Hisat2, Bowtie2, Bwa-Aln, BBMap, Novoalign (this one is commercal, be aware), no real preference, simply stick with BWA-MEM => established tool, well-tested and accepted. Will serve you well.

Answer 2

[lakhujanivijay]

Hi manojkumar_bhosale

I stick to BWA-MEM for exome seq analysis and I completely agree with what ATpoint already said. Just wanted to mention few more reasons -

• well maintained.
• multi-threading supported, hence faster.

[GenoMax]

All tools mentioned by ATPoint are maintained. Most are multi-threaded. There is no real advantage to BWA-MEM other than a well known scientist/developer.

[ATpoint]

As a remark, one could argue that bwa mem might be preferred when one aims to do variant calling given that many workflows expect its output as input, e.g. GATK recommends it. This could save some trouble based on how downstream tools interpret parameters such as MAPQ or certain tags, but this is no real technical argument when it comes to quality of these tools, it is simply what others have built their pipelines on.

Answer 3

[manojkumar_bhosale]

Thanks all for your inputs !!

I got these 3 papers comparing different aligners and it can be said that the BWA is better choice. bowtie2 is comparable to longer reads(>100bp) but there are problems with properly paired reads.

https://www.sciencedirect.com/science/article/pii/S0888754317300204

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619817/

https://www.nature.com/articles/srep17875

Please feel free to update list if you find any newer publication.