quick memo for genome assembly workshop
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- いいね！0
GigaScience
@GigaScience
Daniel Zerbino now talking about file formats, specifically for cancer genomes and the VCF format to report SV. #assemblathon #gaw
2011-03-16 03:21:29
Dawei Lin
@iGenomics
A good representation of variation is particularly important for cancer research. #gaw #assemlathon
2011-03-16 03:21:34
Dawei Lin
@iGenomics
There is significant work has been done to parallelize velvet. #gaw #assemblathon
2011-03-16 03:22:23
The Assemblathon
@assemblathon
Next #gaw talks is Yingrui Li, from BGI-Shenzhen: “NGS de novo assembly: Progresses and challenges”
2011-03-16 03:22:44
BGI Group
@TheBgiGroup
Up next is our very own Yingrui Li with the final talk of the morning: "NGS de novo assembly: Progresses and challenges". #assemblathon #gaw
2011-03-16 03:24:46
Deanna Church (she/her)
@deannachurch
Last talk before lunch: Yingrui Li from BGI to discuss NGS assembly progress and challenges. #gaw
2011-03-16 03:25:15
Scott Edmunds
@SCEdmunds
Yay Yingrui! RT @assemblathon: Next #gaw talks is Yingrui Li, from BGI-Shenzhen: “NGS de novo assembly: Progresses and challenges”
2011-03-16 03:25:40
Dawei Lin
@iGenomics
Yingrui Li, BGI::SOAPdenovo has a similar workflow with other assemblers. differences are in details. #gaw #assemblathon
2011-03-16 03:27:05
BGI Group
@TheBgiGroup
Another plug of BGI's SOAPdenovo tool by Yingrui: http://bit.ly/hLJytc #assemblathon #gaw (& @genomeresearch http://bit.ly/gACJWq)
2011-03-16 03:27:44
Genome Research
@genomeresearch
Velvet currently one of most read Genome Research articles http://bit.ly/gknwLy #gaw
2011-03-16 03:28:39
Dawei Lin
@iGenomics
eliminate errors in original raw reads makes graph much cleaners, use less RAM, reduce load in graph-reduction step,improve reliability #gaw
2011-03-16 03:30:57
GigaScience
@GigaScience
Up now our BGI colleague Yingrui Li discussing reducing graph complexity in his talk on "NGS de novo assembly: progress & challenges" #gaw
2011-03-16 03:31:19
Deanna Church (she/her)
@deannachurch
YL: using 27mers, trying to improve error-correction and use insert sizes that allow reads to overlap. for SOAPdenovo #gaw
2011-03-16 03:31:41
Dawei Lin
@iGenomics
Soapdenovo can use up to 27 kmer size for a reasonable RAM usage. #gaw
2011-03-16 03:32:00
Dawei Lin
@iGenomics
larger kmer up to 12y bp for contiggin to accommodate PE and long reads coming in new technology. #gaw
2011-03-16 03:34:16
BGI Group
@TheBgiGroup
YL showing some error correction examples from (unpublished) oyster genome data amongst other examples. #assemblathon #gaw
2011-03-16 03:35:13
Dawei Lin
@iGenomics
scaffolding performance are hyper sensitive to parameter setting. #gaw #assemblathon
2011-03-16 03:36:16
The Assemblathon
@assemblathon
'scaftigs' intra-scaffold gaps between contigs. #gaw
2011-03-16 03:37:58
Dawei Lin
@iGenomics
Gap closure: based on conservatively constructed scaffolds to make scafigs. #gaw #assemblathon
2011-03-16 03:38:46
Dawei Lin
@iGenomics
Gap closure: add unique regions do not pass stringent filer before, add back repeats. This step has high risk to generate errors. #gaw
2011-03-16 03:41:24
Dawei Lin
@iGenomics
PE reads fill small gaps, characteristics of repeats are considered such as repeat sizes. #gaw #assemblathon
2011-03-16 03:42:58
Scott Edmunds
@SCEdmunds
New word of the day: #scaftigs RT @assemblathon 'scaftigs' intra-scaffold gaps between contigs. #gaw
2011-03-16 03:45:39
Dawei Lin
@iGenomics
smaller kmer size should be used for highly heterogeneous genomes. #gaw #assemblathon
2011-03-16 03:46:05
The Assemblathon
@assemblathon
1 round of assembly now takes only 1 day for human genome on a 256 GB memory node #gaw
2011-03-16 03:47:11
Deanna Church (she/her)
@deannachurch
YL: BGI Developing a cloud based assembler (dev. code: Hecate), cut memory fp to <32G. #gaw
2011-03-16 03:47:24