We assembled a genome around 5GB. Now we are trying to map the Illumina reads to the genome. There are many aligners that can do this job. But which is the fastest one? Have anyone benchmarked any of these tools?
The list of aligners is as follows: short-read aligners.
5 answers
Asking for the fastest tool is posing the question the wrong way.
What you need is finding a fast enough method for your data. As Jeremy points out there are many questions that need to be answered and you will need to run your own tests to identify which tool is fast enough and provides the necessary coverage as well. Your genome is likely to contain vast streches of low complexity regions - that could make some approaches perform differently.
Start with the known fast tools like bowtie and SOAP and see what these do. Also read the literature: Comparative analysis of algorithms for next-generation sequencing read alignment
you need a lot more criteria to make this a fair fight
here are some just off the top of my head
- number of mismatches
- memory ceiling
- paired-end?
- quality-aware?
- sensitivity
your comment indicated that you do not understand that accuracy and sensitivity are not independent from coverage. Increasing these will necessarily slow down the method.
I think it would be interesting to bump it up in 2018.
What is the fastest aligners out there? I have heard (I think Heng Li wrote it somewhere) that with changes in computer architecture, hash-based aligners are coming to be more and more interesting, compared to FM-index based. I am about to try our SNAP, which promises up to 20x increase compared to bowtie2 and bwa.
Like Istvan rightly pointed out, aligner has to be fast for your application. But sometimes speed could be a limiting factor - e.g. when you are teaching a class and want to show something pretty quickly, and not wait for 30 minutes.
I use Novoalign (http://www.novocraft.com/main/page.php?s=novoalign) which is good and fast.
Hi，I‘m using a software named LSC,which need novoalign to align.But I can’t download novoalign.And I can't open tihs URL.Can you send it to me? My email address is liuyanhu005@gmail.com. Many thanks！
hi, please use this page to review the licence agreement and you can download the one which suits your needs best. http://www.novocraft.com/main/page.php?id=968
Thank you a lot!
Hi, My apologies for reviving an old thead but I've receently become aware that the default options in LSC for Novoalign are far from ideal.
If you are using Novoalign with LSC you need to use -r Exhaustive not -r All. This will improve results dramatically and should be better than the other aligners.
For 100bp reads try.. novoalign_options = -c1 -r Ex 1000 -t 120 -F FA -g 0 -x 20 -o sam
If read length is different adjust -t accordingly. On Cerebellum reads used by Kin Fai results are 40% better with 30% reduced run time vs BWA using LSC 0.3.1
Best, Colin
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