emeraldBGC (Deprecated)

Notice: This project has been deprecated and is no longer being maintained. All ongoing and future development has been moved to SanntiS.

emeraldBGC - SMBGC detection tool -

How to use emeraldBGC?

Conda

Requires:

• Linux OS/Unix-like
• InterProScan > 5.52-86.0:
  • https://interproscan-docs.readthedocs.io/en/latest/InstallationRequirements.html Non Linux OS can't run InterProScan. InterProScan output must be provided in TSV or GFF3 format sing "--ip-file" and a GBK as SEQUENCE
• Bioconda: https://bioconda.github.io/user/install.html

Installation

conda create -n emeraldbgc emeraldbgc
conda activate emeraldbgc
conda install -c bioconda emeraldbgc

Basic tests

$ conda activate emeraldbgc
$ emeraldbgc test/files/BGC0001472.fna
$ conda deactivate emerald

Run with interproscan file:

$ conda activate emeraldbgc
$ emeraldbgc --ip-file test/files/BGC0001472.fna.prodigal.faa.gff3 test/files/BGC0001472.fna.prodigal.faa.gb
$ conda deactivate emerald

Docker:

Get InterProsScan data:

The size of download file is ~24G, the final directory is 16G. Be sure to have enough space

$ bash ./get_ips_slim.sh

Docker ready to use script:

Only works if "data/" and emeraldbgc_container.py are in the same directory

$ emeraldbgc_container.py --help
$ emeraldbgc_container.py [OPTIONS] ARGUMENTS

Docker image shell:

$ docker -it --entrypoint bash -v <path to emeraldBGC/docker>/data/:/opt/interproscan quay.io/repository/microbiome-informatics/emerald-bgc
$ emeraldbgc --help
$ emeraldbgc [OPTIONS] ARGUMENTS

Ouput

GFF3 format file

The fields in this header are as follows:

seqname: SeqID of contig, as in prodigal output.
source: emeraldbgc version.
feature: Feature type name, i.e. CLUSTER, CLUSTER_border, CDS.
start: Start position of feature
end: End position of feature
score: empty
strand: empty
frame: empty
attributes:
  ID: ordinal ID for the cluster, beginning with 1.
  nearest_MiBIG: MiBIG accession of the nearest BGC to the cluster in the MIBIG space, measured in Dice dissimilarity coefficient.
  nearest_MiBIG_class: BGC class of nearest_MiBIG.
  nearest_MiBIG_diceDistance: Dice dissimilarity coefficient between ID and nearest_MiBIG.
  score: Post-processing probability output.
  partial: Indicates if a CLUSTER is at the edge of the contig. First and second digits represent 5' and 3' end, respectively. Same as in prodigal's `partial`. "0" shows the cluster is not at the edge, whereas a "1" indicates is at that edge, (i.e. a partial cluster).

Sample:

##gff-version 3
DS999642	EMERALDv0.9.0	CLUSTER	1	136970	.	.	.	ID=DS999642_emrld_1;nearest_MiBIG=BGC0001397;nearest_MiBIG_class=NRP Polyketide;nearest_MiBIG_diceDistance=0.561;partial=10