FW: abyss-1.3.2 compatibility with trans-abyss

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Ka Ming Nip

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Feb 3, 2012, 5:31:38 PM2/3/12

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Hello Trans-ABySS users,

We have been getting quite a few emails and questions lately about filtering and merging assemblies with Trans-ABySS v1.2.0. As some of you may know, we will release v1.3.x soon, but we don't have a set date, yet. However, we have decided that we shall release the filtering and merge scripts (written by Tony Raymond) from v1.3.x in advance.

Please see attached for the scripts.

1. abyss-ta-filter‎ - the script for filtering the assembly and extend junction contigs
Usage: abyss-ta-filter ASSEMBLY_DIR KMER LIB OUT_DIR ISLAND_LEN

ASSEMBLY_DIR = the directory that contains an ABySS assembly
KMER = size of the k-mer used to generate the ABySS assembly
LIB = library name
OUT_DIR = output directory; 3 output files: LIB-f.fa, LIB-j.fa, LIB-contigs.fa
ISLAND_LEN = island size; set this to 151

Requires: abyss-filtergraph, MergeContigs from ABySS 1.3.2

2. abyss-rmdups-iterative - the script for merging all k-assemblies in a directory
Usage: abyss-rmdups-iterative INPUT OUT_DIR LIB

INPUT = the directory that contains the k-directories to be merged
OUT_DIR = the output directory; temp files will be created here, the output file is LIB-contigs.fa
LIB = library name

Requires: abyss-map, abyss-index, MergeContigs from ABySS 1.3.2

Note that the scripts require executables from ABySS 1.3.2. Please set up your environment accordingly.

I advise you to create one output directory for filtering each k-mer assembly and one for merging (if they aren't create already), ie.
k25
k26
...
k49
k50
merge
Then, run abyss-ta-filter on each ABySS assembly. Please specify the output directories as the k-directories created.
Finally, run abyss-rmdups-iterative. Please specify the parent directory of the k-directories as INPUT.

The attached scripts should very likely reflect their counterparts in v1.3.x. However, don't hesitate to modify them to suit your needs.

If you have any questions, please direct them to our Google Group at:
trans...@googlegroups.com

Thanks for using Trans-ABySS.

Ka Ming

abyss-rmdups-iterative

abyss-ta-filter

Ka Ming Nip

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Feb 3, 2012, 7:32:29 PM2/3/12

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Correction.

The script "abyss-ta-filter‎" requires these executables from ABySS
1.3.2
abyss-filtergraph
abyss-junction
MergeContigs