genome improvement and finishing without further sequencing effort
Ruby
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
bin
ext
lib
spec
validation
.document
.gitignore
.gitmodules
.rspec
Gemfile
LICENSE.txt
README.md
Rakefile
VERSION
finishm.gemspec

README.md

WARNING! FinishM is very alpha software and not ready for prime time. There are many unfinished parts of it, and many bugs. Please use with care, and don't judge the authors too harshly.

FinishM

FinishM attempts to improve draft genomes by considering the computational problem to be about finishing, not assembly in the traditional sense.

A finishing approach to assembly

Metagenome and isolate assemblers generate contigs from reads, but still leave valuable information on the table. FinishM exploits this information to improve/finish a draft genome without any further laboratory-based work.

In even a moderately successful assembly, resultant contigs constitute the vast majority of the genome being sequenced, but this fact is ignored by assemblers. Unlike a traditional assembler FinishM does not attempt to directly extend contigs, but instead focuses on connecting already assembled contigs.

FinishM has several modes:

  • Attempt to improve a genome. See finishm roundup. This mode fulfills both the wander and gapfill modes.
  • Determine which contig ends are connected in the assembly graph. See finishm wander.
  • FinishM 'gapfills' (replaces N characters) using a graph-theoretic approach that appears to outperform current gapfilling programs. See finishm gapfill.
  • Sometimes a human is better able to interpret an assembly graph than a machine. FinishM creates human interpretable graph visualisations that let humans solve assembly problems. See finishm visualise.
  • Some other experimental de-novo (non-finishing) metagenome assembly techniques are implemented in finishm assemble.

Installation

First, you'll need Ruby (FinishM is tested on 2.1). Then to install:

gem install finishm

FinishM also has some external dependencies:

  • clustalo (for gapfilling/roundup)
  • GraphViz (for the visualise mode)

Usage

After installation, a listing of the modes and their usage:

finishm

Developing

To hack on finishm:

git clone https://github.com/wwood/finishm.git
cd finishm
bundle install
git submodule update --init
cd ext/src
git checkout -b finishm origin/finishm #possibly this step is not required for newer versions of git
make MAXKMERLENGTH=255 finishm velveth velvetg
cp obj/shared/libfinishm.so.1.0 ../../lib/external/
cd ../..
./bin/finishm -h

Citation

A manuscript describing the tools described here is currently in preparation. However, FinishM reuses code from velvet, clustalo and BioRuby, so these tools may be worth citing.

Copyright

Copyright (c) 2012-2015 Ben J. Woodcroft. See LICENSE.txt for further details.