Resources to boost your bioinformatics toolkit. With a special focus in meta'omics oriented tools.

CLOUD: a non-parametric detection test for microbiome outliers: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0514-4

Anvi'o: https://merenlab.org/2016/06/26/installation-v2/

Big_Scape: https://git.wageningenur.nl/medema-group/BiG-SCAPE/-/wikis/installation

Big_Mex: https://github.com/pereiramemo/BiG-MEx/wiki

DESeq2: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily): https://github.com/rrwick/Bandage/wiki

Antismash: https://docs.antismash.secondarymetabolites.org/install/

Kaiju: https://kaiju.binf.ku.dk/

phyloFLash: http://hrgv.github.io/phyloFlash/

gggenomes (A grammar of graphics for comparative genomics): https://thackl.github.io/gggenomes/

EnrichM (comparative genomic tools for MAGs): https://github.com/geronimp/enrichM

Siamcat (machine learning for microbiome): https://www.biorxiv.org/content/10.1101/2020.02.06.931808v1.full

GToTree (phylogenomics): https://github.com/AstrobioMike/GToTree/wiki/what-is-gtotree%3F

Binny (automatic binning for complex metagenomics datasets): https://www.biorxiv.org/content/10.1101/2021.12.22.473795v1.full

Microbe Annotator: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03940-5

An introduction to phylogenomics (astrobiomike): https://astrobiomike.github.io/genomics/phylogenomics Amplicon (astrobiomike): https://astrobiomike.github.io/amplicon/ Metagenomics (astrobiomike): https://astrobiomike.github.io/genomics/ Assemblies with anvi'o (astrobiomike): https://astrobiomike.github.io/metagenomics/metagen_anvio (includes: To coassemble or not to coassmble)

Babraham bioinformatics: https://www.bioinformatics.babraham.ac.uk/training.html

Short read quality and trimming: https://angus.readthedocs.io/en/2018/quality-and-trimming.html

Next-Gen Sequence Analysis workshop: https://angus.readthedocs.io/en/2018/toc.html

Revse Ecology Analysis on Microbiome: https://cran.r-project.org/web/packages/RevEcoR/vignettes/RevEcoR.html

GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): https://sites.google.com/site/mb3gustame/

Importing KEGGs on Anvi'o: https://merenlab.org/2018/01/17/importing-ghostkoala-annotations/

Doing meta-analysis in R: https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/

https://www.frontiersin.org/articles/10.3389/fgene.2019.01344/full (Computational methods to integrate macroecology of microbes)

https://genome.cshlp.org/content/early/2020/03/18/gr.258640.119 (meren) https://www.frontiersin.org/articles/10.3389/fmicb.2018.01635/full https://www.nature.com/articles/s41597-020-00617-9 https://www.nature.com/articles/s41396-020-0622-6 https://peerj.com/articles/8614/ (termites) https://www.nature.com/articles/s42003-020-0856-x.pdf (mags and ecology) https://www.nature.com/articles/s41587-021-01130-z#Abs1 (lineage resolved MAGS)

https://www.biorxiv.org/content/10.1101/2020.06.30.180448v6 (Chiara Vanni)

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000731 (Arctic Oceans) https://pubmed.ncbi.nlm.nih.gov/12946402/ (Evolution of secondary metabolites)