Shotgun metagenomics analysis- links and papers

#1 Read based approach https://huttenhower.sph.harvard.edu/metaphlan/

https://huttenhower.sph.harvard.edu/humann/

https://www.mg-rast.org/

https://kaiju.binf.ku.dk/results/6240-3130714759

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46

#2 Assembly-based approach and alternative pipelines https://github.com/franciscozorrilla/metaGEM?tab=readme-ov-file

https://github.com/franciscozorrilla/unseenbio_metaGEM

https://github.com/bxlab/metaWRAP

https://academic.oup.com/bioinformatics/article/34/17/i884/5093234

https://academic.oup.com/view-large/figure/408321447/BIOINFORMATICS_34_17_i884_f1.png

https://academic.oup.com/bioinformatics/article/31/10/1674/177884

https://github.com/ablab/spades

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03585-4

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01213-8#Sec16

https://github.com/Ecogenomics/CheckM

https://gtdb.ecogenomic.org/

https://www.nature.com/articles/s41592-022-01431-4

#3 Functional analysis https://academic.oup.com/bioinformatics/article/30/14/2068/2390517

https://github.com/bbuchfink/diamond

http://eggnog5.embl.de/#/app/home

#4 MUST read-- perfect summary of all the tools

https://academic.oup.com/bib/article/22/5/bbab030/6184411