Bambus2
Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. The original Bambus package was the first general purpose scaffolders made available as an open source package. We are happy to announce the arrival of Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.
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 reproduced here Bambus 2.0/quick start guide.
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