Difference between revisions of "Metagenomics"
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| − | ==Comparison of species composition | + | ==Comparison of species composition from shotgun metagnomic data== |
<br /> | <br /> | ||
* Read classification (kraken-like): needs normalization by genome length to derive relative abundance | * Read classification (kraken-like): needs normalization by genome length to derive relative abundance | ||
| − | |||
| + | == Tools == | ||
| − | === | + | === Species Composition === |
====mOTUs2 <cite>motus2</cite> ==== | ====mOTUs2 <cite>motus2</cite> ==== | ||
| Line 17: | Line 17: | ||
<br /> | <br /> | ||
| − | ==== Bracken ==== | + | ==== Bracken <cite>lu2019</cite> ==== |
| + | ==== MetaPhlan2 <cite>metaphlan</cite> ==== | ||
| + | |||
| + | === Taxonomic asssignation of contigs === | ||
| + | |||
| + | ==== CAT/BAT <cite>CAT</cite> ==== | ||
| + | |||
| + | * Consensus of ORF taxonomy | ||
==links== | ==links== | ||
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<biblio> | <biblio> | ||
#motus2 pmid=30833550 | #motus2 pmid=30833550 | ||
| + | #metaphlan pmid=26418763 | ||
| + | #lu2019 LU, Jennifer, BREITWIESER, Florian P., THIELEN, Peter, et al. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science, 2017, vol. 3, p. e104. [https://peerj.com/articles/cs-104/] | ||
| + | #CAT https://github.com/dutilh/CAT | ||
</biblio> | </biblio> | ||
Latest revision as of 10:46, 5 June 2019
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
Bracken [2]
MetaPhlan2 [3]
Taxonomic asssignation of contigs
CAT/BAT [4]
- Consensus of ORF taxonomy
links
Bibliography
- 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 |
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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]
- 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 |