Index of /examples/bioinformatics/velvet

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] test_reads.sam 08-Mar-2015 20:46 28M [   ] chr2R.fa 08-Mar-2015 20:48 21M [   ] test_reads.fa 08-Mar-2015 20:46 8.5M [   ] test_long.fa 08-Mar-2015 20:46 249K [   ] test_reference.fa 08-Mar-2015 20:46 99K [   ] velvet_job.qsub 09-Oct-2015 16:22 285 [DIR] out_dir/ 08-Mar-2015 20:48 -

Velvet package example

To run velvet at the command line:

scc4% module load velvet/1.2.10

scc4% velveth

scc4% velveth out_dir 21 -fasta -short test_reads.fa
[0.000001] Reading FastA file test_reads.fa;
[0.176000] 142858 sequences found
[0.176010] Done
[0.189199] Reading read set file out_dir/Sequences;
[0.208116] 142858 sequences found
[0.301888] Done
[0.301908] 142858 sequences in total.
[0.302571] Writing into roadmap file out_dir/Roadmaps...
[0.325778] Inputting sequences...
[0.325790] Inputting sequence 0 / 142858
[0.914128] === Sequences loaded in 0.590048 s
[0.923880] Done inputting sequences
[0.923908] Destroying splay table
[0.940675] Splay table destroyed


To submit a job, execute command:
scc4% qsub -P my_project velvet_job.qsub


Manual for Velvet:
https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf