Workflow Type: Common Workflow Language
Stable

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.

Documentation: https://docs.mgnify.org/en/latest/analysis.html#assembly-analysis-pipeline

Inputs

ID Name Description Type
contigs n/a n/a
  • File
contig_min_length n/a n/a
  • int
ssu_db n/a n/a
  • File
lsu_db n/a n/a
  • File
ssu_tax n/a n/a
  • string
lsu_tax n/a n/a
  • string
ssu_otus n/a n/a
  • string
lsu_otus n/a n/a
  • string
rfam_models n/a n/a
  • string[]
rfam_model_clans n/a n/a
  • string
other_ncrna_models n/a n/a
  • string[]
ssu_label n/a n/a
  • string
lsu_label n/a n/a
  • string
5s_pattern n/a n/a
  • string
5.8s_pattern n/a n/a
  • string
CGC_config n/a n/a
  • string
CGC_postfixes n/a n/a
  • string[]
cgc_chunk_size n/a n/a
  • int
protein_chunk_size_eggnog n/a n/a
  • int
protein_chunk_size_hmm n/a n/a
  • int
protein_chunk_size_IPS n/a n/a
  • int
func_ann_names_ips n/a n/a
  • string
func_ann_names_hmmer n/a n/a
  • string
HMM_gathering_bit_score n/a n/a
  • boolean
HMM_omit_alignment n/a n/a
  • boolean
HMM_name_database n/a n/a
  • string
hmmsearch_header n/a n/a
  • string
EggNOG_db n/a n/a
  • string
EggNOG_diamond_db n/a n/a
  • string
EggNOG_data_dir n/a n/a
  • string
InterProScan_databases n/a n/a
  • string
InterProScan_applications n/a n/a
  • string[]
InterProScan_outputFormat n/a n/a
  • string[]
ips_header n/a n/a
  • string
ko_file n/a n/a
  • string
Uniref90_db_txt n/a n/a
  • string
diamond_maxTargetSeqs n/a n/a
  • int
diamond_databaseFile n/a n/a
  • string
diamond_header n/a n/a
  • string
go_config n/a n/a
  • string
graphs n/a n/a
  • string
pathways_names n/a n/a
  • string
pathways_classes n/a n/a
  • string
gp_flatfiles_path n/a n/a
  • string
clusters_glossary n/a n/a
  • string

Steps

ID Name Description
before-qc n/a n/a
after-qc n/a n/a
touch_file_flag n/a n/a
touch_no_cds_flag n/a n/a

Outputs

ID Name Description Type
qc-status n/a n/a
  • File
qc_summary n/a n/a
  • File
hashsum_input n/a n/a
  • File
qc-statistics_folder n/a n/a
  • Directory
compressed_files n/a n/a
  • File[]
index_fasta_file n/a n/a
  • File?
bgzip_index n/a n/a
  • File?
bgzip_fasta_file n/a n/a
  • File?
chunking_nucleotides n/a n/a
  • File[]?
chunking_proteins n/a n/a
  • File[]?
functional_annotation_folder n/a n/a
  • Directory?
stats n/a n/a
  • Directory?
pathways_systems_folder n/a n/a
  • Directory?
pathways_systems_folder_antismash n/a n/a
  • Directory?
pathways_systems_folder_antismash_summary n/a n/a
  • Directory?
sequence-categorisation_folder n/a n/a
  • Directory?
taxonomy-summary_folder n/a n/a
  • Directory?
rna-count n/a n/a
  • File?
completed_flag_file n/a n/a
  • File?
no_cds_flag_file n/a n/a
  • File?
no_tax_flag_file n/a n/a
  • File?

Version History

v5.0.7 (latest) Created 7th Jun 2022 at 09:03 by Martin Beracochea

Fix collect_scripts.py


Frozen v5.0.7 981aafc

master @ 981aafc (earliest) Created 7th Jun 2022 at 08:41 by Martin Beracochea

Fix collect_scripts.py


Frozen master 981aafc
help Creators and Submitter
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Additional credit

Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Submitter
Discussion Channel
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Views: 140

Created: 7th Jun 2022 at 08:41

Last updated: 7th Jun 2022 at 09:04

Last used: 28th Jun 2022 at 22:09

help Attributions

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Total size: 367 MB
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