Stars
Open source code for AlphaFold 2.
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
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A nextflow pipeline to detect AMR determinants and mobile genetic elements.
Identifies mobile genetic elements from genome assemblies and predicts likely associated AMR genes
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
Identification of Mobile Elements in Enterococcae with a Focus on AMR Genes
demo workflow to detect mobile genetic elements in metagenomes
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)
geNomad: Identification of mobile genetic elements
LANL-Bioinformatics / PhaME
Forked from sanahmed/PhaMEGiven a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (gene…
Massively parallel phylogenetic placement of genetic sequences
Phylogenetic orthology inference for comparative genomics
Downloads videos and playlists from YouTube
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Automated pipeline for whole bacterial genome analysis based on snakemake
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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