Workflow for abyss assembly

[Dave]

Anyone know where I can find a simple workflow for using Abyss?
Specifically, the steps that you take with each of the programs that
are included with the abyss distribution. I've searched around and
read the Abyss papers but I seem to be missing how to proceed after
running ABYSS.

Thanks,
Dave

[Alejandro Sanchez]

Hi Dave,

Basically, the pipeline goes like this:

ABYSS - the single-end assembler
AdjList - finds overlaps of length k-1 between contigs
PopBubbles - collapses variation
----o-----
KAligner - aligns reads to contigs
ParseAligns - finds pairs of reads in alignments
DistanceEst - estimates distances between contigs
Overlap - find overlaps between blunt contigs
SimpleGraph - finds paths between pairs of contigs
MergePaths - merges consistent paths
MergeContigs

If you have unpaired reads, then ABYSS will be run creating contigs. If
you have paired reads, abyss-pe is a makefile that first, will assemble
as your reads as unpaired with ABYSS and then, mapped them back to the
contigs continuing the pipeline from KAligner to the creation of the
consensus.

There is a README in the abyss directory that is pretty clear on how to
run it.

Cheers.

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[D Sidote]

Alejandro,

Thanks for the info. It seems I was looking for something more complicated when the answer was staring me in the face. For some reason it never occurred to me that the list was the order to run the programs in.

Thanks again!

[Shaun Jackman]

Hi Dave,

You can use the driver script abyss-pe to run the component programs of
ABySS. The option -n,--dry-run of abyss-pe is useful to display the
commands that abyss-pe would run without actually running them.

In actual fact, abyss-pe is a Makefile script and -n,--dry-run is an
option of make.

Cheers,
Shaun

[D Sidote]

Shaun,

This is useful information. Thanks!

Dave