This is the central repository of public MGX pipelines.
Field description:
- Name: Short pipeline name
- Description: Pipeline description
- Author: Pipeline maintainer
- URL: Web site with additional pipeline information
- Version: Pipeline version
- File: Conveyor workflow for read-based analysis
- File2: Conveyor workflow for gene annotation
All pipelines should use 0-based coordinates when creating sequence
observations.
Name |
Description |
Author |
URL |
version |
file |
file2 |
MGX default taxonomy |
MGX default taxonomic classification based on Kraken and Diamond vs. RefSeq proteins |
Sebastian Jaenicke |
- |
1.0 |
mgx_default_taxonomy.xml |
|
Centrifuge |
Centrifuge: rapid and sensitive classification of metagenomic sequences |
Sebastian Jaenicke |
- |
1.0 |
centrifuge.xml |
mgxgene_centrifuge.xml |
Kaiju |
Kaiju: Fast and sensitive taxonomic classification for metagenomics |
Sebastian Jaenicke |
- |
1.0 |
kaiju.xml |
mgxgene_kaiju.xml |
Kraken |
Kraken: ultrafast metagenomic sequence classification using exact alignments |
Sebastian Jaenicke |
- |
1.0 |
kraken.xml |
|
KrakenUniq |
Taxonomic sequence classification with KrakenUniq |
Sebastian Jaenicke |
- |
1.0 |
krakenuniq.xml |
|
Kraken 2 |
Kraken: ultrafast metagenomic sequence classification using exact alignments |
Sebastian Jaenicke |
- |
1.0 |
kraken2.xml |
mgxgene_kraken2.xml |
MetaPhlAn 4 |
MetaPhlAn 4 marker-based taxonomic classification |
Sebastian Jaenicke |
- |
1.0 |
metaphlan4.xml |
|
16S Pipeline |
Classification of 16S rRNA fragments |
Sebastian Jaenicke |
|
1.0 |
rdp_pipeline.xml |
|
Name |
Description |
Author |
URL |
version |
file |
file2 |
COG |
COG-based functional classification |
Sebastian Jaenicke |
- |
1.0 |
eggnog.xml |
mgxgene_eggnog.xml |
SwissProt EC numbers |
EC number annotation based on best-Blast-hit vs. SwissProt database |
Sebastian Jaenicke |
- |
1.0 |
ecnumber.xml |
mgxgene_ecnumber.xml |
FunGene HMM search |
HMM search vs. FunGene functional genes |
Sebastian Jaenicke |
- |
1.0 |
fungene.xml |
mgxgene_fungene.xml |
dbCAN |
Automated Carbohydrate-active enzyme annotation based on dbCAN |
Sebastian Jaenicke |
- |
1.0 |
dbCAN_besthit.xml |
mgxgene_dbcan.xml |
ClusterMine360 |
PKS/NRPS analysis based on BLAST vs ClusterMine360 database |
Sebastian Jaenicke |
- |
1.0 |
clustermine360.xml |
mgxgene_clustermine360.xml |
Pfam |
Annotate best Pfam domain hit |
Sebastian Jaenicke |
- |
1.0 |
pfam_besthit.xml |
mgxgene_pfam.xml |
TIGRFAMS |
Annotate best TIGRFAMS domain hit |
Sebastian Jaenicke |
- |
1.0 |
tigrfam_besthit.xml |
mgxgene_tigrfam.xml |
PGAP |
Annotate best NCBI PGAP HMM hit |
Sebastian Jaenicke |
- |
1.0 |
pgap.xml |
mgxgene_pgap.xml |
MIBiG |
MIBiG secondary metabolite screening |
Sebastian Jaenicke |
- |
1.0 |
mibig.xml |
mgxgene_mibig.xml |
KOfam |
KO number annotation |
Sebastian Jaenicke |
- |
1.0 |
kofam.xml |
mgxgene_kofam.xml |
UniRef50 |
UniRef50 annotation |
Sebastian Jaenicke |
- |
1.0 |
uniref50.xml |
mgxgene_uniref50.xml |
VOGDB |
Virus orthologous groups |
Sebastian Jaenicke |
- |
1.0 |
- |
mgxgene_vogdb.xml |
Name |
Description |
Author |
URL |
version |
file |
file2 |
ARDB |
Antibiotic resistance gene annotation using best Blast hit vs. ARDB database |
Sebastian Jaenicke |
- |
1.0 |
ardb.xml |
mgxgene_ardb.xml |
ARG-Annot |
Antibiotic resistance gene annotation using best Blast hit vs. ARG-ANNOT database |
Sebastian Jaenicke |
- |
1.0 |
argannot.xml |
|
BacMet |
Antibacterial biocide- and metal-resistance gene annotation using best Blast hit vs. BacMet database |
Sebastian Jaenicke |
- |
1.0 |
bacmet.xml |
mgxgene_bacmet.xml |
CARD |
Antibiotic resistance gene screening using Blast vs CARD (Comprehensive antibiotic resistance database) |
Sebastian Jaenicke |
- |
1.0 |
card.xml |
mgxgene_card.xml |
MVirDB |
MvirDB-based virulence analysis |
Sebastian Jaenicke |
- |
1.0 |
mvirdb.xml |
mgxgene_mvirdb.xml |
AMRFinder+ |
NCBI AMRFinder+ |
Sebastian Jaenicke |
- |
1.0 |
- |
mgxgene_amrfinder.xml |
Name |
Description |
Author |
URL |
version |
file |
FR-HIT |
Fragment recruitment based on NCBI Magic-BLAST |
Sebastian Jaenicke |
- |
1.0 |
blastn_refmap.xml |
Bowtie2 |
Bowtie2-based reference mapping |
Sebastian Jaenicke |
- |
1.0 |
bowtie_refmap.xml |
Blast-Mapping |
Fragment recruitment employing FR-HIT |
Sebastian Jaenicke |
- |
1.0 |
frhit_refmap.xml |
Name |
Description |
Author |
URL |
version |
file |
16S-Amplicons Bergey |
RDP-based taxonomic assignment for 16S amplicons |
Burkhard Linke |
- |
1.0 |
rdp_amplicons.xml |
Name |
Description |
Author |
URL |
version |
file |
|
|
Sebastian Jaenicke |
- |
1.0 |
besthit_aa.xml |
|
|
Sebastian Jaenicke |
- |
1.0 |
discard_rRNAs.xml |
|
|
Sebastian Jaenicke |
- |
1.0 |
ecolifilter.xml |
|
|
Sebastian Jaenicke |
- |
1.0 |
phageprotscreen.xml |
|
|
Sebastian Jaenicke |
- |
1.0 |
phagescreen.xml |
|
|
Sebastian Jaenicke |
- |
1.0 |
pks.xml |
|
|
Sebastian Jaenicke |
- |
1.0 |
plasmidprotscreen.xml |
|
|
Sebastian Jaenicke |
- |
1.0 |
referencefilter.xml |