search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
763 stars 139 forks source link

Metaviralspades looks for plasmids and not for viruses #577

Open b-brankovics opened 4 years ago

b-brankovics commented 4 years ago

Dear Developers,

I wanted to test metaviralspades on a sample that contains pooled RNA from thousands of plants. Previously, I used regular SPAdes for the assembly which worked quite well. Now, I ran metaviralspades on the same read set and the contigs.fasta file was empty. I can see that there are contigs in K77/contigs_before_metaplasmid.fasta. It appears that metaviralspades.py actually is a metaplasmidspades assembler instead of metaviralspades. Here is the spades.log:

======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:
 * 0:00:21.829    39M / 854M  WARN   ChromosomeRemover        (chromosome_remover.cpp    : 435)   No putative plasmid contigs found!
======= Warnings saved to /~/metaviralspades-def/warnings.log

SPAdes log can be found here: /~/metaviralspades-def/spades.log

Thank you for using SPAdes!

I installed metaviralspades in the following way:

  1. git clone -b metaviral_publication https://github.com/ablab/spades.git metaviralspades
  2. cd metaviralspades; ./assembler/spades_compile.sh
  3. Then used the executable in the bin folder

How could I build the actual metaviralspades assembler instead of the plasmid version?

b-brankovics commented 3 years ago

Alternatively, is it possible to get a compiled version that would run on Ubuntu?

I would really like to use the tool, but I don't know where to get a working version of metaviralspades.

Thanks in advance! :)

Dmitry-Antipov commented 3 years ago

Terribly sorry, I've missed this question.

Metaviral SPAdes was build upon metaplasmid. Both tools are based on iterative low covered edges removal with minor differences in graph simplification and contig output. So, in the publication-support release, most messages were not changed. Of course, we'll fix it in upcoming regular release (within SPAdes package v 3.15).

So, you can use the assemblies you received. Also we strongly recommend to check final contigs with either our viralVerify tool or with CheckV - metaviralSPAdes outputs lots of false-positive contigs by design.