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Merge pull request #72 from EBI-Metagenomics/dev
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Dev
mberacochea authored Nov 29, 2023

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60 changes: 30 additions & 30 deletions README.md
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@@ -7,36 +7,36 @@ Gurbich TA, Almeida A, Beracochea M, Burdett T, Burgin J, Cochrane G, Raj S, Ric
Detailed information about existing MGnify catalogues: https://docs.mgnify.org/src/docs/genome-viewer.html

### Tools used in the pipeline
| Tool/Database | Version | Purpose |
| ----------- | ----------- |----------- |
| CheckM | 1.1.3 | Determining genome quality |
| dRep | 3.2.2 | Genome clustering |
| Mash | 2.3 | Sketch for the catalogue; placement of genomes into clusters (update only); strain tree |
| GUNC | 1.0.3 | Quality control |
| GUNC DB | 2.0.4 | Database for GUNC |
| GTDB-Tk | 2.3.0 | Assigning taxonomy; generating alignments |
| GTDB | r214 | Database for GTDB-Tk |
| Prokka | 1.14.6 | Protein annotation |
| IQ-TREE 2 | 2.2.0.3 | Generating a phylogenetic tree |
| Kraken 2 | 2.1.2 | Generating a kraken database |
| Bracken | 2.6.2 | Generating a bracken database |
| MMseqs2 | 13.45111 | Generating a protein catalogue |
| eggNOG-mapper | 2.1.11 | Protein annotation (eggNOG, KEGG, COG, CAZy) |
| eggNOG DB | 5.0 | Database for eggNOG-mapper |
| Diamond | 2.0.11 | Protein annotation (eggNOG) |
| InterProScan | 5.62-94.0 | Protein annotation (InterPro, Pfam) |
| CRISPRCasFinder | 4.3.2 | Annotation of CRISPR arrays |
| AMRFinderPlus | 3.11.4 | Antimicrobial resistance gene annotation; virulence factors, biocide, heat, acid, and metal resistance gene annotation |
| AMRFinderPlus DB | 3.11 2023-02-23.1 | Database for AMRFinderPlus |
| SanntiS | 0.9.3.2 | Biosynthetic gene cluster annotation |
| Infernal | 1.1.4 | RNA predictions |
| tRNAscan-SE | 2.0.9 | tRNA predictions |
| Rfam | 14.9 | Identification of SSU/LSU rRNA and other ncRNAs |
| Panaroo | 1.3.2 | Pan-genome computation |
| Seqtk | 1.3 | Generating a gene catalogue |
| VIRify | - | Viral sequence annotation |
| MoMofy | 1.0.0 | Mobilome annotation |
| samtools | 1.15 | FASTA indexing |
| Tool/Database | Version | Purpose |
|----------------------------------|------------------|----------- |
| CheckM | 1.1.3 | Determining genome quality |
| dRep | 3.2.2 | Genome clustering |
| Mash | 2.3 | Sketch for the catalogue; placement of genomes into clusters (update only); strain tree |
| GUNC | 1.0.3 | Quality control |
| GUNC DB | 2.0.4 | Database for GUNC |
| GTDB-Tk | 2.3.0 | Assigning taxonomy; generating alignments |
| GTDB | r214 | Database for GTDB-Tk |
| Prokka | 1.14.6 | Protein annotation |
| IQ-TREE 2 | 2.2.0.3 | Generating a phylogenetic tree |
| Kraken 2 | 2.1.2 | Generating a kraken database |
| Bracken | 2.6.2 | Generating a bracken database |
| MMseqs2 | 13.45111 | Generating a protein catalogue |
| eggNOG-mapper | 2.1.11 | Protein annotation (eggNOG, KEGG, COG, CAZy) |
| eggNOG DB | 5.0 | Database for eggNOG-mapper |
| Diamond | 2.0.11 | Protein annotation (eggNOG) |
| InterProScan | 5.62-94.0 | Protein annotation (InterPro, Pfam) |
| CRISPRCasFinder | 4.3.2 | Annotation of CRISPR arrays |
| AMRFinderPlus | 3.11.4 | Antimicrobial resistance gene annotation; virulence factors, biocide, heat, acid, and metal resistance gene annotation |
| AMRFinderPlus DB | 3.11 2023-02-23.1 | Database for AMRFinderPlus |
| SanntiS | 0.9.3.2 | Biosynthetic gene cluster annotation |
| Infernal | 1.1.4 | RNA predictions |
| tRNAscan-SE | 2.0.9 | tRNA predictions |
| Rfam | 14.9 | Identification of SSU/LSU rRNA and other ncRNAs |
| Panaroo | 1.3.2 | Pan-genome computation |
| Seqtk | 1.3 | Generating a gene catalogue |
| VIRify | 2.0.0 | Viral sequence annotation |
| [Mobilome annotation pipeline](https://github.com/EBI-Metagenomics/mobilome-annotation-pipeline) | 2.0.0-rc.1 | Mobilome annotation |
| samtools | 1.15 | FASTA indexing |

## Setup

4 changes: 2 additions & 2 deletions helpers/file_organiser.sh
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@@ -1,6 +1,6 @@
#!/usr/bin/env bash

# The script organises output from the catalogue generation + Virify + Momofy to prepare it for upload to MGnify
# The script organises output from the catalogue generation + Virify + Mobilome annotation pipeline to prepare it for upload to MGnify


function Usage {
@@ -40,7 +40,7 @@ function GenerateRNACentralJSON {
echo "Copying GFFs"
for R in $REPS
do
cp ${RESULTS_PATH}/all_genomes/${R::-2}/${R}/${R}.gff* ${RESULTS_PATH}/additional_data/rnacentral/GFFs/
cp ${RESULTS_PATH}/all_genomes/${R::-2}/${R}/genomes1/${R}.gff* ${RESULTS_PATH}/additional_data/rnacentral/GFFs/
done

echo "Running JSON generation"

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