Bambus2

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.