Metagenomics

Comparison of species composition from shotgun metagnomic data

• Read classification (kraken-like): needs normalization by genome length to derive relative abundance

Tools

Species Composition

mOTUs2 [1]

• Phylogenetic profiling based on universal markers
• Allow to classify genomes for which reference genomes are not available

• relative abundance

Taxonomic asssignation of contigs

CAT/BAT [4]

• Consensus of ORF taxonomy

links

https://lemmi.ezlab.org

Bibliography

1. Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, and Sunagawa S. Microbial abundance, activity and population genomic profiling with mOTUs2. Nat Commun. 2019 Mar 4;10(1):1014. DOI:10.1038/s41467-019-08844-4 |

2. LU, Jennifer, BREITWIESER, Florian P., THIELEN, Peter, et al. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science, 2017, vol. 3, p. e104. [1]

3. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, and Segata N. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015 Oct;12(10):902-3. DOI:10.1038/nmeth.3589 |

4. https://github.com/dutilh/CAT