max BLAST hits too low - Githubissues

rrwick / Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

http://rrwick.github.io/Bandage/

GNU General Public License v3.0

586 stars 98 forks source link

max BLAST hits too low #37

Open rec3141 opened 7 years ago

rec3141 commented 7 years ago

When trying to use a complete bacterial genome as the BLAST query against an assembled genome, Bandage only finds a maximum of 400 hits per query sequence. I don't know if this is a BLAST thing or a Bandage thing, but it would be useful to raise that to a much higher number. My workaround now is to split the query into artificial contigs so that no single contig is saturated.

rrwick commented 7 years ago

I expect it is a BLAST thing, because I just tried the same thing you described and got more than 400 hits per query: screen shot 2017-03-23 at 3 02 09 pm

What version of BLAST do you have? A hacky way to find out which one Bandage is using (in case you have multiple versions installed in different places) is to type rubbish into the command line parameters field: screen shot 2017-03-23 at 3 05 58 pm Then when you search, the resulting error message should state the BLAST version.

I'm using 2.2.31+ and it works for me. If you're on an older version, perhaps try upgrading BLAST? If that doesn't work, I'm not sure...

Ryan

rec3141 commented 7 years ago

Thanks, I updated BLAST and can't reproduce it

rec3141 commented 7 years ago

Ok coming back to this, I'm now on BLAST 2.6.0+ and Bandage 0.8.1 and found the issue cropping up again. Here the same assembly is used as the database. In the first example the query is a full-length bacterial chromosomal sequence, in the second it has been split into records of 10kb each. The coverage of the assembly is much greater in the second instance, and it's not clear why. The files are attached. Any suggestions? Thanks

bandage.zip