quick memo for genome assembly workshop
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- いいね！0
BGI Group
@TheBgiGroup
DJ: PACBIO likely to be great for small genomes, but currently impractical for large genomes as can cost 10X more. #assemblathon #gaw
2011-03-16 02:58:10
Deanna Church (she/her)
@deannachurch
@iGenomics Eric Schadt (from PacBio) made the same point at #AGBT #gaw
2011-03-16 02:58:14
Genome Research
@genomeresearch
Improvement of genome assembly quality http://bit.ly/ff2GaQ #gaw
2011-03-16 02:58:28
Dawei Lin
@iGenomics
ALLPATHS-LG will not work on capillary sequence data. #gaw #assemblathon
2011-03-16 03:01:11
Genome Research
@genomeresearch
Genome assembly using short sequence reads and reduced representation libraries http://genome.cshlp.org/content/20/2/249.abstract #gaw
2011-03-16 03:02:01
Dawei Lin
@iGenomics
Have you evaluated conservative markers across different genomes and different assemblies? #gaw #assemblathon
2011-03-16 03:03:40
The Assemblathon
@assemblathon
Daniel Zerbino from UC Santa Cruz is up next: “Columbus: Templated assembly of partially mapped reads” (keep forgetting hashtags! #gaw)
2011-03-16 03:05:50
Dawei Lin
@iGenomics
ALLPATHS-LG is designed to look forward to use the new recipe not retrofit to legacy sequence data. #gaw #assemblathon
2011-03-16 03:06:57
Deanna Church (she/her)
@deannachurch
Up next, Daniel Zerbino to discuss Hybrid de novo and mapped assembly of short reads. #gaw
2011-03-16 03:07:48
Dawei Lin
@iGenomics
Daniel Zerbino: hybrid de novo & mapped assembly of short read genomics data. #gaw #assemblathon
2011-03-16 03:07:59
Dawei Lin
@iGenomics
Two churches for sequencing individual: mapping vs. de novo #gaw #assemblathon
2011-03-16 03:08:42
BGI Group
@TheBgiGroup
Up now is Daniel Zerbino (UCSC) on a similar theme: "Hybrid de novo and mapped assembly of short read genomic data" #assemblathon #gaw
2011-03-16 03:08:52
Dawei Lin
@iGenomics
Mapping: many tools avalable, assembly: no reference needed, can find novel variant. #gaw
2011-03-16 03:09:30
Dawei Lin
@iGenomics
A reference -assisted de Bruign graph to reduce ambiguity. #gaw
2011-03-16 03:11:23
GigaScience
@GigaScience
Following Daniel Zerbino at #Assemblathon, the Columbus module within Velvet is available here: http://www.ebi.ac.uk/~zerbino/velvet/ #gaw
2011-03-16 03:13:24
Genome Research
@genomeresearch
Zerbino and Birney algorithms for de novo short read assembly using de Bruijn graphs http://bit.ly/dPjCvy #gaw
2011-03-16 03:13:33
Dawei Lin
@iGenomics
Columus: preserve reference structure, use alignment data, allow de novo assembly options. #gaw #assemblathon
2011-03-16 03:14:08
Dawei Lin
@iGenomics
Fusion event confirmed by Berger et al, 2010 Genome Research #gaw #assemblathon
2011-03-16 03:15:26
Deanna Church (she/her)
@deannachurch
DZ: Using the reference structure and de bruijn graphs to capture de novo pieces. #gaw
2011-03-16 03:15:56
BGI Group
@TheBgiGroup
DZ: Relating to the current talk, bit of a write up about the Columbus module within Velvet here: http://ow.ly/4f5lM #gaw #Assemblathon
2011-03-16 03:16:46
Dawei Lin
@iGenomics
Columbus did have longer length than velvet. read mismatches went down because respects difference sin reference genomes #gaw #assemblathon
2011-03-16 03:17:17
Shameer Khader, PhD, MPH
@kshameer
Now following #gaw & #assemblathon (awesome tweeps @deannachurch @iGenomics @BGI_Events ) #genomics #bioinformatics
2011-03-16 03:17:57
Deanna Church (she/her)
@deannachurch
Columbus looks like a module of Velvet http://tinyurl.com/36mfjo7 and is available. #gaw
2011-03-16 03:18:02
The Assemblathon
@assemblathon
Lots of talk about new/different assembly file formats at this meeting. Clearly a need for something which is better than just FASTA #gaw
2011-03-16 03:19:09
Dawei Lin
@iGenomics
Zack Sanbord: breakpoint reassembly, use VC format to report structural variation. #gaw #assemblathon
2011-03-16 03:19:37