MOCAT2

MOCAT2 has been developed at EMBL to process large metagenomic datasets. But can of course also process small datasets. ;)

Please read the full MOCAT (v1.0) article at PLoS ONE or the PDF version.

Processing steps, supported software & ubtegraedt databases:

Quality trimming and filtering of reads
- 3' trimming: FastX and SolexaQA
- 5' trimming: internal scripts

Screen or extract reads against a custom database
- SOAPaligner v2.21

Screen or extract reads against a custom FASTA file
- USEARCH v5/v6

Map reads to a reference database, estimate taxonomic/functional abundance
- SOAPaligner v2.21
- Internal scripts

Assemble high quality reads into contigs and scaftigs
- SOAPdenovo v1.05/v1.06

Revise the assemblies by correcting for indels and chimeric regions
- SOAPdenovo v1.05/v1.06 and BWA v0.7.5a-r16

Predict genes on assembles or revised contigs or scaftigs
- Prodigal v2.60
- MetaGeneMark v2.8

Extract single copy marker genes
- fetchMG v1.0

Cluster genes into reference gene catalogs
- CD-HIT v4.6

Annotate reference gene catalogs
- DIAMOND v0.7.9.58
- The filterBlastReport.pl script from SmashCommunity 1.6

Taxnomic databased integrated in MOCAT2
mOTU-LG: Sunagawa,S. et al. (2013) Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods, 10, 1196–9
specI & NCBI: Mende,D.R. et al. (2013) Accurate and universal delineation of prokaryotic species. Nat. Methods, 10, 881–4.

Pre-compiled reference gene catalogs compatible with MOCAT2
IGC (human gut): Li,J. et al. (2014) An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol., 32, 834–41.
CRC-RGC (human gut): Zeller,G. et al. (2014) Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol. Syst. Biol., 10, 766.
skin-RGC (human skin): Oh,J. et al. (2014) Biogeography and individuality shape function in the human skin metagenome. Nature, 514, 59–64.
mouse-RGC (human skin): Xiao,L. et al. (2015) A catalog of the mouse gut metagenome. Nat Biotech, 33, 1103–1108.
OM-RGC (ocean): Sunagawa,S. et al. (2015) Structure and function of the global ocean microbiome. Science, 348 (6237), 1:10

Functional ddatabases integrated in MOCAT2
eggNOG: Huerta-Cepas, J., et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2015. 10.1093/nar/gkv1248.
ARDB: Liu,B. and Pop,M. (2009) ARDB—Antibiotic Resistance Genes Database. Nucleic Acids Res. , 37 , D443–D447.
CARD: McArthur, A.G., et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 2013;57(7):3348-3357. 10.1128/AAC.00419-13.
DBETH: Chakraborty, A., et al. DBETH: a Database of Bacterial Exotoxins for Human. Nucleic Acid Res. 2012;40 Database issue):D615-20 0.1093/nar/gkr942
dbCAN: Yin, Y., et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2012;40(Web Server issue):W445-451. 10.1093/nar/gks479.
DrugBank: Knox C., et al. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res 2011;39(Database issue):D1035-41. 10.1093/nar/gkq1126
ICEberg: Bi D., et al. ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res. 2012 Jan;40(Database issue):D621-6. 10.1093/nar/gkr846.
KEGG: Kanehisa, M., et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014;42(Database issue):D199-205. 10.1093/nar/gkt1076.
MetaCyc: Caspi, R., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2015. 10.1093/nar/gkv1164.
MvirDB: Zhou, C.E., et al. MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res 2007;35(Database issue):D391-394. 10.1093/nar/gkl791.
PATRIC: Mao, C., et al. Curation, integration and visualization of bacterial virulence factors in PATRIC. Bioinformatics 2015;31(2):252-258. 10.1093/bioinformatics/btu631.
Pfam: Finn, R.D., et al. Pfam: the protein families database. Nucleic Acids Res 2014;42(Database issue):D222-230. 10.1093/nar/gkt1223.
Prophages: Waller, A.S., et al. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J 2014;8(7):1391-1402. 10.1038/ismej.2014.30.
Resfams: Gibson, M.K., et al. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J 9(1). 10.1038/ismej.2014.106.
SEED subsystems: Overbeek, R., et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014;42(Database issue):D206-214. 10.1093/nar/gkt1226.
Superfamily: Gough, J., et al. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001;313(4):903-919. 10.1006/jmbi.2001.5080.
vFam: Skewes-Cox, P., et al. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One 2014;9(8):e105067. 10.1371/journal.pone.0105067.
VFDB: Chen, L., et al. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 2012;40(Database issue):D641-645. 10.1093/nar/gkr989.
Victors: Mao, C., et al. Curation, integration and visualization of bacterial virulence factors in PATRIC. Bioinformatics 2015;31(2):252-258. 10.1093/bioinformatics/btu631.

MOCAT2 v2.0 has a number of great new features. With this version you can easily generate functional and taxonomic profiles of your metagenomes, as well as generate and annotate reference gene catalogs. Functional profiles are generated by mapping reads to one of the included, environment specific databases (human gut, human skin, mouse gut or the oceans), or by generating your own gene catalog and map the reads to that. Taxonomic profiles are generated by either mapping reads to the RefMG.v1 database, which contains single copy marker genes from bacterial genomes, and then generating profiles for NCBI taxonomic levels. This is useful if you want to have a species assignment of the taxa in your metagenomes. Or, a second approach, mapping reads to the mOTU database. By doing this you will get abundances of the species clusters described in Mende et al. (2013). This approach will generate well defined species clusters abundances, and enable you to discover new species in the metagenome, but not all of these clusters can be taxonomically assigned. This version also supports the extraction of marker genes, describedon the homepage for Taxonomic profiling using mOTUs.