Pipelines¶
This page lists the Nextflow pipelines developed by the Microbiome Informatics team.
mettannotator¶
No description
Repository: EBI-Metagenomics/mettannotator
mobilome-annotation-pipeline¶
No description
Repository: EBI-Metagenomics/mobilome-annotation-pipeline
amplicon-pipeline¶
No description
Repository: EBI-Metagenomics/amplicon-pipeline
Modules Used¶
- cmsearchtbloutdeoverlap
- cutadapt
- easel/eslsfetch
- extractcoords
- fastqsuffixheadercheck
- infernal/cmsearch
- krona/ktimporttext
- librarystrategycheck
- mapseq
- mapseq2biom
- pimento/generatebcv
- seqfu/check
Subworkflows Used¶
miassembler¶
No description
Repository: EBI-Metagenomics/miassembler
Modules Used¶
genomes-generation¶
No description
Repository: EBI-Metagenomics/genomes-generation
biosiftr¶
BioSIFTR - Biome-specific Shallow-shotgun Inference of Functional Traits through Read-mapping
Repository: EBI-Metagenomics/biosiftr
Modules Used¶
datascout¶
This repo queries and gather data from different resources which can then be used to run bulk automatised annotation of microbial genomes.The different types of data are: OrthoDB and UniProt orthology data; Rfam (non coding Rna data); Transcriptomic data from ENA
Repository: EBI-Metagenomics/datascout
edna¶
No description
Repository: EBI-Metagenomics/edna
raw-reads-analysis-pipeline¶
Raw Reads Analysis Pipeline
Repository: EBI-Metagenomics/raw-reads-analysis-pipeline
Modules Used¶
- bwamem2/mem
- cmsearchtbloutdeoverlap
- easel/eslsfetch
- extractcoords
- infernal/cmsearch
- krona/ktimporttext
- mapseq
- mapseq2biom
- samtools/bam2fq
Subworkflows Used¶
assembly-analysis-pipeline¶
MGnify Assembly Analysis Pipeline
Repository: EBI-Metagenomics/assembly-analysis-pipeline
Modules Used¶
- catpack/contigs
- cmsearchtbloutdeoverlap
- combinedgenecaller/merge
- dbcan/easysubstrate
- diamond/blastp
- downloadfromfire
- dram/distill
- easel/eslsfetch
- extractcoords
- filterpaf
- fraggenescanrs
- generategaf
- genomeproperties
- infernal/cmscan
- infernal/cmsearch
- interproscan
- keggpathwayscompleteness
- krona/ktimporttext
- mgnifypipelinestoolkit/kronatxtfromcatclassification
- mgnifypipelinestoolkit/rheachebiannotation
- mgnifypipelinestoolkit/summarisegoslims
- minimap2/align
- owltools
- sanntis
- seqkit/grep
Subworkflows Used¶
- assembly_decontamination
- combined_gene_caller
- contigs_taxonomic_classification
- decontaminate_contigs
- detect_rna
- goslim_swf
datagrabber¶
No description
Repository: EBI-Metagenomics/datagrabber
emg-viral-pipeline¶
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Repository: EBI-Metagenomics/emg-viral-pipeline
genomes-catalogue-pipeline¶
MGnify genome analysis pipeline
Repository: EBI-Metagenomics/genomes-catalogue-pipeline
motus_pipeline¶
Raw reads mOTUs and taxonomic classification pipeline
Repository: EBI-Metagenomics/motus_pipeline
mgnifams¶
No description
Repository: EBI-Metagenomics/mgnifams
reference-databases-preprocessing-pipeline¶
No description
Repository: EBI-Metagenomics/reference-databases-preprocessing-pipeline
mgbinrefinder¶
Bin refinment tool
Repository: EBI-Metagenomics/mgbinrefinder
microeuks-gene-benchmarker¶
Scripts to benchmark the outputs from gene annotation tools for microbial eukaryotes
Repository: EBI-Metagenomics/microeuks-gene-benchmarker
causal_multi-omics_recommender¶
No description
Repository: EBI-Metagenomics/causal_multi-omics_recommender
miniqc-pipeline¶
No description
Repository: EBI-Metagenomics/miniqc-pipeline
deciphon-benchmark¶
Baseline benchmark.
Repository: EBI-Metagenomics/deciphon-benchmark
iseq-prof-chlamydia¶
Chlamydia benchmark.
Repository: EBI-Metagenomics/iseq-prof-chlamydia
iseq-prof-workflow¶
No description
Repository: EBI-Metagenomics/iseq-prof-workflow