MAGScoT = MAG Scoring (and refinement) Tool
MAGScoT is pronounced like "Mascot".
MAGScoT is a fast tool for the scoring and refinement of metagenomic bins from different binning tools. The MAGScoT article has been published in Bionformatics.
In brief, MAGScoT uses GTDBtk rel 207 (v2) marker genes to score completeness and contamination of metagenomic bins, to iteratively select the best metagenome-assembled genomes (MAGs) in a dataset. In addition, MAGScoT can merge overlapping metagenomic bins from multiple binning inputs and add these hybrid bins for scoring and refinement to the set of candidates MAGs.
MAGScoT outperforms existing tools on levels of computation time and resources, as well as quality and quanitity of recovered MAGs.
$ Rscript MAGScoT.R
Usage: MAGScoT.R [options]
Options:
-i CHARACTER, --input=CHARACTER
Tab-separated input file with three columns: bin, contig, set; no header!
--hmm=CHARACTER
Tab-separated input file with marker mapping; three columns: gene id, marker, e-value.
Gene IDs must represent contig IDs after removal of _[0-9] at the end of the name (prodigal default)
-p CHARACTER, --profile=CHARACTER
Profile used for scoring, all derived from GTDB release 207. default[=bac120+ar53], ar53, bac120. [default]
-o CHARACTER, --out=CHARACTER
output file name base [default=MAGScoT]
-a SCORE_A, --score_a=SCORE_A
Scoring parameter a [default=1]
-b SCORE_B, --score_b=SCORE_B
Scoring parameter b [default=0.5]
-c SCORE_C, --score_c=SCORE_C
Scoring parameter c [default=0.5]
-t THRESHOLD, --threshold=THRESHOLD
Scoring minimum completeness threshold [default=0.5]
--score_only
Only do scoring, no refinement [false]
--skip_merge_bins
Skip bin merging [false]
-m MIN_MARKERS, --min_markers=MIN_MARKERS
Minimum number of unique markers in bins to be considered as seed for bin merging [default=25]
-s MIN_SHARING, --min_sharing=MIN_SHARING
Minimum percentage of shared markers for bin sharing. [default=0.8]
-n N_ITERATIONS, --n_iterations=N_ITERATIONS
Number of merging iterations to perform. [default=2]
-h, --help
Show this help message and exit
MAGScoT can be run in a conda environment
conda create -n MAGScoT_env
conda activate MAGScoT_env
conda install mamba
mamba install -c conda-forge -c bioconda -c r r-base r-optparse r-dplyr r-readr r-funr hmmer prodigal parallel
git clone https://github.com/ikmb/MAGScoT
MAGScoT_folder="/path/to/MAGScoT"
cd $MAGScoT_folder/example
Rscript $MAGScoT_folder/MAGScoT.R -i example.contigs_to_bin.tsv --hmm example.hmm
Alternatively, MAGScoT can be run via the Docker Container.
MAGScoT_folder="/path/to/MAGScoT"
docker run -v `pwd`:`pwd` ikmb/magscot:latest -i $MAGScoT_folder/example/example.contig_to_bin.tsv --hmm $MAGScoT_folder/example/example.hmm
MAGScoT_folder="/path/to/MAGScoT"
cd $MAGScoT_folder/example
### ORF detection with prodigal
zcat example.contigs.fasta.gz | prodigal -p meta -a example.prodigal.faa -d example.prodigal.ffn -o tmpfile
### ALTERNATIVE: Fast parallel ORF detection with prodigal
# mkdir -p tmp_workfolder
# zcat example.contigs.fasta.gz | parallel -j 8 --block 999k --recstart '>' --pipe prodigal -p meta -a tmp_workfolder/example.{#}.faa -d tmp_workfolder/example.{#}.ffn -o tmpfile
# cat tmp_workfolder/example.*.faa > example.prodigal.faa
# cat tmp_workfolder/example.*.ffn > example.prodigal.ffn
# rm -r tmp_workfolder tmpfile
### annotation of protein sequences using HMMer and GTDBtk r207 marker genes
hmmsearch -o example.hmm.tigr.out --tblout example.hmm.tigr.hit.out --noali --notextw --cut_nc --cpu 8 $MAGScoT_folder/hmm/gtdbtk_rel207_tigrfam.hmm example.prodigal.faa
hmmsearch -o example.hmm.pfam.out --tblout example.hmm.pfam.hit.out --noali --notextw --cut_nc --cpu 8 $MAGScoT_folder/hmm/gtdbtk_rel207_Pfam-A.hmm example.prodigal.faa
cat example.hmm.tigr.hit.out | grep -v "^#" | awk '{print $1"\t"$3"\t"$5}' > example.tigr
cat example.hmm.pfam.hit.out | grep -v "^#" | awk '{print $1"\t"$4"\t"$5}' > example.pfam
cat example.pfam example.tigr > example.hmm
individual contig to bin files from binning algorithms
Format: BIN<tab>CONTIG
E.g.: metabat_bin_01<tab>contig_20
awk '{print $1"\t"$2"\tvamb"}' example.vamb.contigs_to_bin.tsv > example.contigs_to_bin.tsv
awk '{print $1"\t"$2"\tconcoct"}' example.concoct.contigs_to_bin.tsv >> example.contigs_to_bin.tsv
awk '{print $1"\t"$2"\tmetabat2"}' example.metabat2.contigs_to_bin.tsv >> example.contigs_to_bin.tsv
awk '{print $1"\t"$2"\tmaxbin2"}' example.maxbin2.contigs_to_bin.tsv >> example.contigs_to_bin.tsv
Final contig to bin file for all algorithms
Format: BIN<tab>CONTIG<tab>BINNER
E.g: metabat_bin_01<tab>contig_20<tab>metabat
Rscript $MAGScoT_folder/MAGScoT.R -i example.contigs_to_bin.tsv --hmm example.hmm
Final contig to bin file for all algorithms
Format: BIN<tab>CONTIG<tab>BINNER
E.g: metabat_bin_01<tab>contig_20<tab>metabat
The project was funded by the German Research Foundation (DFG) Collaborative Research Center 1182 - Origin and Function of Metaorganisms and DFG Research Unit 5042 - miTarget.
