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Old 09-02-2009, 10:22 PM   #1
henry
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Smile about burrows-wheeler transform

Hi, guys,

I'm working on next-generation sequencing data (illumina, and solid). It's said that bwa can run very fast. I've downloaded bwa. But I don't know how to install it. I'm using federa on x64 computer. Is there anyone who could kindly tell me how to install it?

Can bwa process solid data efficiently? Could you guys give me any suggestion about what software I may use to process solid data of whole human genome? Thank you very much.

Jing
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Old 09-02-2009, 10:40 PM   #2
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sorry, i made a mistake. i was using install commands for maq to install bwa. just enter the bwa file and key in make, it works fine.

anyway, Can bwa process solid data efficiently? Could you guys give me any suggestion about what software I may use to process solid data of whole human genome? Thank you very much.

Jing
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Old 09-03-2009, 10:50 AM   #3
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Originally Posted by henry View Post
sorry, i made a mistake. i was using install commands for maq to install bwa. just enter the bwa file and key in make, it works fine.

anyway, Can bwa process solid data efficiently? Could you guys give me any suggestion about what software I may use to process solid data of whole human genome? Thank you very much.

Jing
I would run some quick simulations to convince yourself that bwa can detect what you are looking for, especially SNPs and indels in the presence of errors. Also note that SOLiD data has a higher raw color error rate (up to 10%), whereas BWA says it is suited for <%2 error rates. Anyhow, you are sacrificing something for speed and in my own unpublished simulations it is sensitivity, though BWA is oddly faster for ABI data compared to Illumina data (maybe I am doing something wrong). To my knowledge, simulation tools can be found in any of the following alignment packages: MAQ, BFAST, and SAMtools. Feel free to PM me if you want to discuss further.
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Old 09-03-2009, 11:23 AM   #4
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You might wish to try NextGENe which will process Solid and other data and has a modified BWT for whole genome reference, or we can send a BWT reference to you.

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Old 09-03-2009, 08:43 PM   #5
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I would run some quick simulations to convince yourself that bwa can detect what you are looking for, especially SNPs and indels in the presence of errors. Also note that SOLiD data has a higher raw color error rate (up to 10%), whereas BWA says it is suited for <%2 error rates. Anyhow, you are sacrificing something for speed and in my own unpublished simulations it is sensitivity, though BWA is oddly faster for ABI data compared to Illumina data (maybe I am doing something wrong). To my knowledge, simulation tools can be found in any of the following alignment packages: MAQ, BFAST, and SAMtools. Feel free to PM me if you want to discuss further.
Hi, nilshomer
Thank you for replying to me. ABI provides a free software named 'CORONALite' to process SOLiD data. I tried using 'CORONALite' to identify SNPs/indels from small model organism genome as a test. It could identify SNPs, but no indels were found. I felt the results were strange.
Plus CORONALite use PBS to assign work submited to our computer cluster, so the work can be performed on multiple computer nodes. However, some assignment on some node couldn't be finished successfully (I don't know the reason. Maybe many people were competing to use that computer node. I have no idea). Then I had to submit work again and again. CORONALite is not that good.
I didn't try to process SOLiD data with MAQ. But MAQ claims it can process SOLiD data. BWA is somewhat improved version of MAQ. So I wanna have a try. BWA is suited for process SOLiD data with error rates less than 2%, but SOLiD data has a raw color error rate (up to 10%). So BWA is also not a good option for processing SOLiD data.
I'm confused that there isn't any good open source software that can be applied to process SOLiD data?
Thank you very much.

Jing
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Old 09-03-2009, 08:54 PM   #6
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You might wish to try NextGENe which will process Solid and other data and has a modified BWT for whole genome reference, or we can send a BWT reference to you.

Best
Hi SoftGenetics,
Thank you very much. I've downloaded BWT references.
Best
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Old 09-03-2009, 09:25 PM   #7
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Quote:
Originally Posted by henry View Post
Hi, nilshomer
Thank you for replying to me. ABI provides a free software named 'CORONALite' to process SOLiD data. I tried using 'CORONALite' to identify SNPs/indels from small model organism genome as a test. It could identify SNPs, but no indels were found. I felt the results were strange.
Plus CORONALite use PBS to assign work submited to our computer cluster, so the work can be performed on multiple computer nodes. However, some assignment on some node couldn't be finished successfully (I don't know the reason. Maybe many people were competing to use that computer node. I have no idea). Then I had to submit work again and again. CORONALite is not that good.
I didn't try to process SOLiD data with MAQ. But MAQ claims it can process SOLiD data. BWA is somewhat improved version of MAQ. So I wanna have a try. BWA is suited for process SOLiD data with error rates less than 2%, but SOLiD data has a raw color error rate (up to 10%). So BWA is also not a good option for processing SOLiD data.
I'm confused that there isn't any good open source software that can be applied to process SOLiD data?
Thank you very much.

Jing
Try BFAST (http://bfast.sourceforge.net), which is admittedly my own software. I am the processing NextGene, I will let you know how that goes. I have also evaluated BWA, MAQ, SHRiMP, SOCS, and ZOOM. As per corona-lite, I think there is a "small-indel" tool you can download from the solid software tools website. We have not gotten corona-lite to work in our lab so I feel your pain.
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Old 09-03-2009, 11:09 PM   #8
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Try BFAST (http://bfast.sourceforge.net), which is admittedly my own software. I am the processing NextGene, I will let you know how that goes. I have also evaluated BWA, MAQ, SHRiMP, SOCS, and ZOOM. As per corona-lite, I think there is a "small-indel" tool you can download from the solid software tools website. We have not gotten corona-lite to work in our lab so I feel your pain.
Hi, nilshhomer,
I've downloaded the software you suggested, and had a glimpse of the manual. I will have a try.
Btw, you mentioned you evaluated BWA, MAQ, SHRiMP, SOCS, and ZOOM on next-generation data (illumina, solid). Have compared them with BFAST ? If possible, could send me the evaluation results for those tools? Thank you very much!
Anyway, maybe I will compare the results produced by BAW with those results by BFAST.

Best

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Old 09-04-2009, 08:10 AM   #9
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Originally Posted by henry View Post
Hi, nilshhomer,
I've downloaded the software you suggested, and had a glimpse of the manual. I will have a try.
Btw, you mentioned you evaluated BWA, MAQ, SHRiMP, SOCS, and ZOOM on next-generation data (illumina, solid). Have compared them with BFAST ? If possible, could send me the evaluation results for those tools? Thank you very much!
Anyway, maybe I will compare the results produced by BAW with those results by BFAST.

Best

Jing
It goes without saying that the purpose of the evaluations was to compare other methods to BFAST for SOLiD data. PM me with your email and I will send you a draft.

Nils
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Old 09-05-2009, 12:40 AM   #10
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It goes without saying that the purpose of the evaluations was to compare other methods to BFAST for SOLiD data. PM me with your email and I will send you a draft.

Nils
hi, nilshhomer,
Thank you for your kind help. I will read the draft carefully. My email is zhangj@big.ac.cn
Best wishes

Jing
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