Other - jsgounot/metagenomic-pipelines GitHub Wiki

All-in-one packages / pipelines

• EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research
• mettannotator is a bioinformatics pipeline that generates an exhaustive annotation of prokaryotic genomes using existing tools (ENA)

PanGenome construction and comparison

• Roary: rapid large-scale prokaryote pan genome analysis
• Parsnp - Core-genome alignment and analysis (part of Harvest)

Nanopore Assemblies

• FPA: Filter Pairwise Alignment
• YACRD: Yet Another Chimeric Read Detector

Circular genome

Check whether a genome is circular or not.

Potential tools :

• Circlator: A full time assembler
• Simple-Circularise: This one seems way faster
• Flye provides this information after assembly
• VRCA: ViRal and Circular content from metAgenomes

Personal notes

• I tried Simple-Circularise but output result is not really convincing, not sure how efficient is this tool
• VRCA runs well and is quite fast but I don't know of results quality

Potential methods :

Mapping reads using minimap2 for example (long or short) and detecting multi-mapped reads in both extremity.

Clustering

• Random Forest Classifier: Can be used to identify variations between two conditions, for example with abundance vaklues (but you need to identify features first ? ALDEx2) [see here]
• Aldex2: ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq

• pvclust: An R package for hierarchical clustering with p-values

R packages

• Use center-log ratio (transformation) to normalize data [see here and here]
• Analysis of Phylogenetics and Evolution (APE): PCA and other methods [see here]
• Use of UniFrac distance paper: Beta diversity of a sample using phylogeny information. Can be done using python.

Statistics

• A Practical Guide to Statistical Power and Sample Size Calculations in R.
• When to use t-test vs MWU