Genome Assembly

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We are currently evaluating software and algorithms for microbial genome assembly.


Some important papers to read on genome assembly:

http://www.ncbi.nlm.nih.gov/pubmed/18576944 (Alternate link)

http://www.ncbi.nlm.nih.gov/pubmed/18349386 (Alternate link)


Video tutorials on genome assembly can be found at [1] under the heading "Informatics on High Throughput Sequencing".

MIRA Assembly

Assembly 454 data

Computer memory needs a few Gs (2 to 5 about) in order to run (Using <miramem> to estimate).

"Novel Clostridium sp" genome was assembled

Contig # 959
Average length 5405.81
Maximum length 45779

Compare with "Newbler" assembly

Contig # 1119
Average length 3973
Maximum length 33180

Velvet Assembly

Requirements (from Velvet Manual) Velvet should function on any standard 64bit Linux environment with gcc. A good amount of physical memory (12GB to start with, more is no luxury) is recommended. It can in theory function on a 32bit environment, but such systems have memory limitations which might ultimately be a constraint for assembly.

Statistics of "Novel Clostridium sp" genome assembly with Velvet

number of contigs 8197
max contig length 626
avg contig length 244.65

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