01 April 2013

Bradyrhizobium and Aphaenogaster

Next post Previous post

April Fool's notes


Prepped Aphaenogaster samples for shipping to BMGC for sequencing.


After correcting velvet assembler to specify that data format was fastq (not fasta), de novo assembly went quickly, ~ 1 hr run time!

Found online tool velvet advisor to help with k-mer selection. Based on my inputs of 12.5 million reads, paired-end, each read 60bp long, estimated genome size of 9 Mbp, recommended k=53. For 30 fold k-mer coverage, recommended k=51

Results for different k-mers. Assembly length is for contigs > 999 bp

k-mer num_contigs 50% coverage quantile assembly length contigs >999 (Mbp)
21 13,853 88.2
31 3,065 90
41 1,695 71
53 1,946 45 8.16e6

velvetOptimiser looks like a nice defensible way to go about selecting k-mer…but not implemented in Galaxy.

Another good reason to (finally!) migrate to command-line.

Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.