Genome Assembly
From Bioinformatics.Org Wiki
We are currently evaluating software and algorithms for microbial genome assembly.
- ALLPATHS - http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development
- SHARCGS - http://sharcgs.molgen.mpg.de
- MIRA - http://www.chevreux.org/projects_mira.html
- Velvet - http://www.ebi.ac.uk/~zerbino/velvet
- Edena - http://www.genomic.ch/edena
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
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