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 -
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
conda create -n emeraldbgc emeraldbgc
conda activate emeraldbgc
conda install -c bioconda emeraldbgc$ conda activate emeraldbgc
$ emeraldbgc test/files/BGC0001472.fna
$ conda deactivate emeraldRun 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$ bash ./get_ips_slim.sh$ emeraldbgc_container.py --help
$ emeraldbgc_container.py [OPTIONS] ARGUMENTS$ docker -it --entrypoint bash -v <path to emeraldBGC/docker>/data/:/opt/interproscan quay.io/repository/microbiome-informatics/emerald-bgc
$ emeraldbgc --help
$ emeraldbgc [OPTIONS] ARGUMENTSGFF3 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