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Old 08-01-2012, 02:23 AM   #1
me91
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Question next generation sequencing simulation softwares

Hi
I need a next generation sequencing simulation software.
I'v worked with "metasim" before but it has lots of bugs and does not work well!!
I would be glad if somebody introduces best softwares.
thank you all
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Old 08-01-2012, 11:54 AM   #2
kamsen
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Have a look at http://www.seqan.de/projects/mason/.
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Old 08-01-2012, 12:06 PM   #3
adaptivegenome
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dgwsim is a good one by nils homer
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Old 08-01-2012, 12:13 PM   #4
rnaseek
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For simulating RNA-Seq data there BEERS by a group from U.PENN.
http://cbil.upenn.edu/BEERS/
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Old 08-02-2012, 01:23 AM   #5
me91
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thank you all

and witch one is suitable for simulating very long reads to get long stream of SNPs ?
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Old 12-14-2012, 03:43 AM   #6
raj.musunuri
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try ART
http://www.niehs.nih.gov/research/re...tatistics/art/
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Old 02-11-2013, 06:34 AM   #7
Ana Suárez
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Dear all,

I am using MetaSim which doesn't produce .qual files. As explained at the FAQs, all inserted errors/substitutions are reported in the fasta header per read, that look like that:

>r1.1 |SOURCES={GI=320159410,bw,1206304-1206640}|ERRORS={52_1:C,89_1:A,90_1:G,90_2:T,216_1:T}|SOURCE_1="Anaerolinea thermophila UNI-1" (0d34b7871fbf039b0739d6497bb075cffa74a470)

Do you know any way to generate a .qual file from that information?

Many thanks in advance!
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Old 02-14-2013, 12:04 AM   #8
syfo
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You can find more in the wiki
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