quick memo for genome assembly workshop

The UC Santa Cruz Assemblathon analysis is available here: http://t.co/HYy3SAu #gaw #assemblathon

2011-03-16 02:33:17

The UC Santa Cruz Assemblathon talk is now available here: http://t.co/tsmMThN #gaw #assemblathon

2011-03-16 02:34:05

SG: modify K-mer size across genome. Use small K for increased sensitivity and bigger K for increased specificity. #gaw #assemblathon

2011-03-16 02:38:31

ALLPATHS-LG can assembly 1G genome for 1 week using 512GB RAM computer. #assemblathon #gaw

2011-03-16 02:40:06

Criteria for evaluation: continuity (N50), completeness (% genome,exome), ,and accuracy (error rate) #assemblathon #gaw

2011-03-16 02:43:05

Scaffold comparison: ALLPATHS-LG is better that capillary data. Completeness comparison is similar. #assemblathon #gaw

2011-03-16 02:45:14

Segmental duplication completeness: capillary is better. #assemblathon #gaw

2011-03-16 02:46:19

DJ: segmental duplication- the bane of whole genome assembly #gaw #assemblathon

2011-03-16 02:46:39

Genome Research @genomeresearch

Assembly of large genomes using second-generation sequencing http://bit.ly/ft5G4s #assemblathon #gaw

2011-03-16 02:48:13

per 10k base error rate 1.2 for ALLPATHS-LG, 5.1 for capillary #assemblathon #gaw

2011-03-16 02:48:26

DJ: ALLPATH-LG better per base accuracy than capillary- better sequence coverage and assembler error correction. #gaw #assemblathon

2011-03-16 02:49:52

local missaseebly rate: 2.2% and 2.7% for ALLPATHS-LG and capillary. #assemblathon #gaw

2011-03-16 02:49:59

tried 15 vertebrates (7 fish and & mammals) : for variation between genomes, fish are harder. #assemblathon #gaw

2011-03-16 02:51:23

You can find out much more about the #gaw meeting by following @igenomics he is tweeting lots more info than me!

2011-03-16 02:52:38

DJ: Longer links (i.e. fosmid size) really helps improve scaffold N50 #gaw #assemblathon // underscores need for tech improvment

2011-03-16 02:53:24

Genome Research @genomeresearch

Thanks! RT @assemblathon: You can find out much more about the #gaw meeting by following @igenomics he is tweeting lots more info than me!

2011-03-16 02:53:51

Fosmid physical coverage 20x provides more consistent scaffold size. #assemblathon #gaw

2011-03-16 02:54:11

DJ: To fully know a person's genome, you need de novo assembly! #gaw #assemblathon

2011-03-16 02:54:20

“@deannachurch: DJ: To fully know a person's genome, you need de novo assembly! #gaw #assemblathon”

2011-03-16 02:54:45

BGI Group @TheBgiGroup

DJ: Fish harder to assemble: more polymorphic, repeat structure harder, more recalcitrant sequences. Whole genome duplications? #gaw

2011-03-16 02:55:38

Dropping #assemblathon tag, tired of typing two tags. Sticking with #gaw

2011-03-16 02:55:40

Good recipe for cheap assembly: 45X fragment 100bp, 45X jump 2kbp, 5X long jump 6Kbp, 2X 40kb jump. #assemblathon #gaw

2011-03-16 02:56:01