Thursday, 24 December 2009

De novo assembly with ABI SOLiD reads

Ran a trial run with sample data!

perl --run fragment --file fixed-saet/reads.csfasta
./velveth_de output_directory/ 21 -short /home/kev/bin/source/solid-denovo-acc-tools/output/ -strand_specific

./velvetg_de output_directory/ -read_trkg yes -amos_file yes
./ --afgfile Velvet_asm.afg --csfasta colorspace_input.csfasta --run fragment

denovoadp sample_input 200 > sample_output
Voila! base space!
doing more testing will update post with remarks later

@ Victor,
you may be able to find denovoadp here but its a new version and I have yet to test it  
SOLiD™ System de Novo Assembly Tools 2.0 The tools in this project provide the ability to create de novo assemblies from SOLiD™ colorspace reads.

1 comment:

  1. Where can I get denovoadp. I succeeded with everything except that


Datanami, Woe be me