Difference between revisions of "Bambus2"
From AMOS WIKI
(Created page with 'Getting data into Bambus 2 can be a pain. Here is my recipe: toAmos \ -s my.fa \ -c my.contig \ -m my.mates \ -o my.afg You need the .fa to list the contigs withi…') |
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| − | For more details, see the info here: http://www.cbcb.umd.edu/software/bambus/ | + | For more details, see the info here: http://www.cbcb.umd.edu/software/bambus/, which I have dumped here [[Bambus 2.0/quick start guide]]. |
Revision as of 11:20, 16 December 2010
Getting data into Bambus 2 can be a pain. Here is my recipe:
toAmos \ -s my.fa \ -c my.contig \ -m my.mates \ -o my.afg
You need the .fa to list the contigs within the GFD-like contig file (annoying but true). You don't need accurate sequences in the .fa, you just need something to make the format valid. The .contig and .mates are as expected for Bambus.
The resulting .afg is then 'banked' with:
bank-transact -c \ -b my.bnk \ -m my.afg
For more details, see the info here: http://www.cbcb.umd.edu/software/bambus/, which I have dumped here Bambus 2.0/quick start guide.
