ABySS

We have Assembly By Short Sequences – a de novo, parallel, paired-end sequence assembler installed on Odyssey. The version on Odyssey is 1.1.2.

To submit your ABySS jobs:

[hptc@iliadaccess04 ~]$ module load hpc/abyss-1.1.2

Loading module hpc/openmpi-1.3.2_gnu-4.1.2.



        hpc/abyss-1.1.2

        ****************************************************



          This module sets up the environment for:



            ABySS version 1.1.2

            ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.



          Use the command:



            module display hpc/abyss-1.1.2



          to see exactly what this module does.



        ****************************************************

[hptc@iliadaccess04 ~]$ bsub -q long_parallel -n 32 -a openmpi -e s_2_abyss.e -o s_2_abyss.o -J s_2_abyss abyss-pe np=32 k=63 n=10 in='s_2_1.fasta s_2_2.fasta' name=s_2_abyss