Short read aligners

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ryan_m
ryan_m's picture
Short read aligners

I have tried most of the Solexa/illumina capable free short read aligners (e.g. Eland, MAQ, Novoalign, Shrimp, BWA, Bowtie, SOAP, Mosaik) and have had variable degrees of success/satisfaction with them.  I generally flip-flop between MAQ and Novoalign but BWA may prove to replace MAQ in the near future.  I am wondering if anyone who has bought into the commercial alignment software could share their stories.  I'm interested to know if there are real benefits to forking over the money for a license to these programs (some examples are the Synamatix package or the commercial version of Novoalign).  Anyone with positive or negative feedback on the commercial tools is welcome to post their comments here.
Thanks,

Ryan

G_nome
G_nome's picture
I have tried BWA aligner but

I have tried BWA aligner but did not succeed in getting the index to run:
bwa index -a bwtsw human_all.fasta
[bwa_index] Pack FASTA... 57.96 sec
[bwa_index] Reverse the packed sequence... 18.37 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncConstructFromPacked] 10 iterations done. 99999987 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999987 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999987 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399999987 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 499999987 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 599999987 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 699999987 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 799999987 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 899999987 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 999999987 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1099999987 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1199999987 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 1299999987 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1399999987 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1499999987 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1599999987 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999987 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1799999987 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1899999987 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 1999999987 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2099999987 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2199999987 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2299999987 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2399999987 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2499999987 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2599999987 characters processed.
[BWTIncConstructFromPacked] 270 iterations done. 2699999987 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2799999987 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2899999987 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 2999999987 characters processed.
[bwt_gen] Finished constructing BWT in 309 iterations.
[bwa_index] 3126.33 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[BWTIncConstructFromPacked] 10 iterations done. 99999987 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999987 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999987 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399999987 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 499999987 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 599999987 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 699999987 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 799999987 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 899999987 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 999999987 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1099999987 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1199999987 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 1299999987 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1399999987 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1499999987 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1599999987 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999987 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1799999987 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1899999987 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 1999999987 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2099999987 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2199999987 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2299999987 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2399999987 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2499999987 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2599999987 characters processed.
[BWTIncConstructFromPacked] 270 iterations done. 2699999987 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2799999987 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2899999987 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 2999999987 characters processed.
[bwt_gen] Finished constructing BWT in 309 iterations.
[bwa_index] 3324.13 seconds elapse.
[bwa_index] Update BWT... Segmentation fault
 
I am running this on a machine with 64G of RAM so it can't be a memory issue.  Has anyone else seen this (the fasta file is hg18).

Thanks
 

zee
zee's picture
Chances are with Synamatix's

Chances are with Synamatix's applications you will never get to try them out outside of their web interface and it's also very expensive.
With novoalign you're paying a small fee for added extras and prioritized software support, usage advice, etc.  The cost of a license is not that much more than a run on the GAII machine itself, and you get to process the data faster than you can sequence it. Lots of open source software will work great but you're at the mercy of developers when you request some extra features/benefits or need prioritized help.
The money you're paying is essentially for those extras and the developer's support.  If you can think of a feature that would benefit your own work a paid-for license could get that feature incorporated in the produce Free of charge. This has happened on one occasion.
Another point worth mentioning is that paid-for software only has real value if it somehow does a better job than Open Source Software in terms of the user's needs.
 

ryan_m
ryan_m's picture
Thanks for your comments zee.

Thanks for your comments zee. 
Ryan

zhlu1986
zhlu1986's picture
Hello,Ryan, now I have a

Hello,Ryan, now I have a problem the same as yours.
When I use bwa to index reference sequence,thers is a fault:
……
segmentation fault
……
How do you solve your problem?
Many thanks.
ps. My reference is converted from database format to fasta format using blast fasta cmd.It is 4.93GB.