10 April 2013

genome assembly, Bradyrhizobium, and velvet

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still assembling

Aphaenogaster

Permits…

Bradyrhizobium

Sample	Oligo
IC1	ATCACG
ENC4	TTAGGC
EWC3	CGATGT

VelvetOptimiser gives error and doesn’t complete final run due to error:

Unable to open /panfs/roc/groups/2/tiffinp/stanton1//home/tiffinp/stanton1/B-elkanii-genomes/velvet-assembly-EWC3/VelOpt_data_49/stats.txt for exp_cov determination.
at /home/tiffinp/stanton1/software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838

Problem was with script…had specified entire path ‘/home/tiffinp/stanton1/B-elkanii-genomes/velvet-assembly-EWC3’ when I should have only specified the relative path ‘B-elkanii-genomes/velvet-assembly-EWC3’. Once I fixed this, ran perfectly!

Reran with corrected script and worked perfectly!

Sample	kmer	Number contigs	N50	Total length
IC1	49	1,424	44,314	9,513,597
ENC4	45	2,196	64,938	8,479,608
EWC3	45	1,309	65,438	8,418,993

ToDo

1. Order velvet contigs to B. japonicum USDA110 reference genome using …?
2. Mapping assembly to existing B. elkanii genomes using Bowtie2
3. Compare de novo to mapping assemblies using MUMmer
4. Gene annotation…using RAST?
5. Phylogeny with all sequenced Bradyrhizobium strains
   • do strains from C. fasciculata group together or interspersed with strains from soybean?

Reading

Van Heerwaarden, B. & Sgrò, C.M. (2013). Multivariate analysis of adaptive capacity for upper thermal limits in Drosophila simulans. Journal of Evolutionary Biology, 26, 800–809. Retrieved April 10, 2013,

Workflow

Zotero. Installed AutoZotBib to allow for automatic export of a bibtex file built from my Zotero library. There was a note that this may considerably slow down Zotero so will test it out before committing fully.

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Latex style files for PLOS and Genome Biology: http://ligarto.org/rdiaz/

LaTeX bst files
LaTeX bst (bibliography styles) files for Public Library of Science, Biology and Genome Biology. The PLoS one I use with the natbib package (with \usepackage[authoryear, round, sort]{natbib} in the preamble. The GB one does not use natbib. To use either, include

  \bibliography{the.name.of.the.bib.file}
  \bibliographystyle{GenomeBiology} %% or PLoS

where you want the bibliography to appear. I prepared these bst files using makebst.tex, with a little manual editing. (makebst.tex is available, I think, as standard in all LaTeX installations for GNU/Linux, and also from CTAN). If you find any errors, I'd appreciate if you can let me know.

Computing

Ubuntu finally installed on Dell T7600 workstation! The awesome computer techs at Pine Computers ended up having to completely replace the RAID card to get one with linux drivers. Picked up machine and booted perfectly!