contributors:team_4_page
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision | Next revision Both sides next revision | ||
|
contributors:team_4_page [2015/05/11 08:58] emfeal [Running ABySS] |
contributors:team_4_page [2015/05/11 09:01] emfeal [Running ABySS] |
||
|---|---|---|---|
| Line 99: | Line 99: | ||
| </code> | </code> | ||
| Note that the parallel version of ABySS requires two things in particular: | Note that the parallel version of ABySS requires two things in particular: | ||
| - | * **(1)** The use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | + | * **(1)** The use of a parallel environment which can be selected using a qsub option. |
| + | * **(2)** The //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | ||
| + | The parallel environment option in the script above: | ||
| <code> | <code> | ||
| #$ -pe mpi 10 | #$ -pe mpi 10 | ||
| Line 107: | Line 109: | ||
| qconf -spl | qconf -spl | ||
| </code> | </code> | ||
| - | * **(2)** The //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | ||
| abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are: | abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are: | ||
| Line 166: | Line 167: | ||
| * konnector: fill the gaps between paired-end reads by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph | * konnector: fill the gaps between paired-end reads by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph | ||
| * abyss-bloom: construct reusable bloom filter files for input to Konnector | * abyss-bloom: construct reusable bloom filter files for input to Konnector | ||
| - | |||
| =====ABySS pipeline===== | =====ABySS pipeline===== | ||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
