Package: gecco-tool
Hi, I'm GECCO!🦎 ️OverviewGECCO (Gene Cluster prediction with Conditional Random Fields) is a fast and
scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs)
in genomic and metagenomic data using Conditional Random Fields (CRFs).🔧 Installing GECCOGECCO is implemented inPython, and supportsall
versionsfrom Python 3.7. It requires
additional libraries that can be installed directly fromPyPI, the Python Package Index.Usepipto install GECCO on your
machine:$pipinstallgecco-toolIf you'd rather useConda, a package is available
in thebiocondachannel. You can install
with:$condainstall-cbiocondageccoThis will install GECCO, its dependencies, and the data needed to run
predictions. This requires around 40MB of data to be downloaded, so
it could take some time depending on your Internet connection. Once done,
you will have ageccocommand available in your $PATH.Note that GECCO usesHMMER3, which can only run
on PowerPC and recent x86-64 machines running a POSIX operating system.
Therefore, GECCO will work on Linux and OSX, but not on Windows.🧬 Running GECCOOncegeccois installed, you can run it from the terminal by giving it a
FASTA or GenBank file with the genomic sequence you want to analyze, as
well as an output directory:$geccorun--genomesome_genome.fna-osome_output_dirAdditional parameters of interest are:--jobs, which controls the number of threads that will be spawned by
GECCO whenever a step can be parallelized. The default,0, will
autodetect the number of CPUs on the machine usingos.cpu_count.--cds, controlling the minimum number of consecutive genes a BGC region
must have to be detected by GECCO. The default is3.--threshold, controlling the minimum probability for a gene to be
considered part of a BGC region. Using a lower number will increase the
number (and possibly length) of predictions, but reduce accuracy. The
default of0.8was selected to optimize precision/recall on a test set
of 364 BGCs fromMIBiG 2.0.--cds-feature, which can be supplied a feature name to extract genes
if the input file already contains gene annotations instead of predicting
genes withPyrodigal. A common value
for records downloaded from GenBank is--cds-feature CDS.🔎 ResultsGECCO will create the following files:{genome}.genes.tsv: Thegenesfile, containing the genes extracted
or predicted from the input file, and per-gene BGC probabilities
predicted by the CRF.{genome}.features.tsv: Thefeaturesfile, containing the identified
domains in the input sequences, in tabular format.{genome}.clusters.tsv: If any were found, aclustersfile, containing
the coordinates of the predicted clusters along their putative biosynthetic
type, in tabular format.{genome}_cluster_{N}.gbk: If any were found, a GenBank file per cluster,
containing the cluster sequence annotated with its member proteins and domains.GECCO can also convert results to other formats that may be more convenient
depending on the downstream usage. GECCO can convert results into:GFF3 format so they can be loaded into a genomic viewer
(gecco convert clusters --format gff).GenBank files with antiSMASH-style features so they can be loaded intoBiG-SLiCEfor further analysis
(gecco convert gbk --format bigslice).FASTA files with the sequences of all the predicted BGCs (gecco convert gbk --format fna)
or with the sequences of all their proteins (gecco convert gbk --format faa).To get a more visual way of exploring of the predictions, you
can open the GenBank files in a genome editing software likeUGENE.
You can otherwise load the results into an AntiSMASH report: check theIntegrationspage of the
documentation for a step-by-step guide.🔖 ReferenceGECCO can be cited using the following preprint:Accurate de novo identification of biosynthetic gene clusters with GECCO.
Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller.
bioRxiv 2021.05.03.442509;doi:10.1101/2021.05.03.442509💭 Feedback⚠️ Issue TrackerFound a bug ? Have an enhancement request ? Head over to theGitHub issue
trackerif you need to report
or ask something. If you are filing in on a bug, please include as much
information as you can about the issue, and try to recreate the same bug
in a simple, easily reproducible situation.🏗️ ContributingContributions are more than welcome! SeeCONTRIBUTING.mdfor more details.⚖️ LicenseThis software is provided under theGNU General Public License v3.0or later. GECCO is developped by theZeller Teamat theEuropean Molecular Biology Laboratoryin Heidelberg.