Extract scaffold info from Mira PE 454 assembly?

[pmiguel]

Does Mira create scaffolds during paired-end read sequence assemblies? gsAssembler does, so I just assumed Mira would. But maybe I need to run downstream software (Bambus?) to extract this information?

--
Phillip

[sklages]

No, MIRA doesn't create scaffolds; you should use an external tool like BAMBUS.

cheers,
Sven

[themerlin]

You can use the MIRA output for scaffolding with Bambus (see tutorial)

http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf

You can also use the MIRA output with SSPACE with only minimal manipulation:

http://www.baseclear.com/sequencing/data-analysis/bioinformatics-tools/sspace/

J

[pmiguel]

Bambus Obsolete?

I am getting the mysterious "script failed" error mentioned in this thread:

http://seqanswers.com/forums/showthread.php?p=21874

Therein it is posited that there is some maximum number of contigs that can be processed. Anyone know what that maximum is or have other insights?

Also, given that no modifications to Bambus have been checked in to its SourceForge site since 2005 -- isn't this really a pre-next gen program?

--
Phillip

[pmiguel]

Bambus works for gsAssembler .ace file

On the other hand, for smaller 454 jobs it does work for Mira assemblies. And with a few modifications of the normal protocol, works directly on a gsAssembler .ace file.

Not sure if gsAssembler creates a .ace file by default. If not, use the appropriate option to have one created. Then create the .contig file from the .ace file as normal using the amostools utility:

ace2contig -i 454Contigs.ace 454Contigs.contig

The ace file created by gsAssembler uses a different paradigm to denote forward and reverse reads. So I used the following 454Contigs.mates file:

library all     1000    6000    (.......).*
pair    (.*)_left       (.*)_right

As always for bambus, the field delimiter (shown above as whitespace) for a .mates must be tabs. So a copy/paste from this post will not work without modification of the resultant file.

perl -i -pe 's/  */\t/g' 454Contigs.mates

should do the trick. Note that is two spaces prior to the "*", not one. If you only put one, that would allow perl to place a tab in between every character.

One other catch for me. I had been skipping the .conf file, allowing goBambus to substitute its own default one. But I got the following this time:

Step 400: Running scaffolder
Error: Priority not specified: at least one library must be assigned a priority in module grommit
Grommit(/usr/local/bambus-2.33/bin/grommit -i 454Contigs_bambus.inp -o 454Contigs_bambus.out.xml -C 454Contigs_bambus.grommit.conf --append --logfile goBambus.log --debug 1) script failed

So I created a .conf file, 454Contigs_bambus.conf with the following in it:

# Priorities
priority ALL 1

# Redundancies
redundancy 2

# min group size
mingroupsize 0

Then the following command:

goBambus -c 454Contigs.contig -m 454Contigs.mates -o 454Contigs_bambus -C 454Contigs_bambus.conf

appears to work.

Of course, gsAssembler should create scaffolds itself. But, for this project it did a very poor job, creating a few tiny scaffolds. So it is nice to have Bambus as a backup.

--
Phillip