⚡ ♒ Rapid prokaryotic genome annotation

Trinity RNA-Seq de novo transcriptome assembly

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Extensive de-novo TE Annotator

DEPRECATED: This repository is now frozen - please see individual lesson repositories.

TransDecoder source

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

NOVOPlasty - The organelle assembler and heteroplasmy caller

🌳 Create a tree using Mash distances

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/

📈 Automatically optimise three of Velvet's assembly parameters.

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)

scripts to parse and analyse MCScanX collinearity output

A toolkit for annotation of transposable element families from unassembled sequence reads

Identify phage regions in bacterial genomes for masking purposes

Workflows for correcting and scaffolding long-read (PacBio, nanopore) genome assemblies using optical mapping and/or Dovetail Hi-C data

Make a non-redundant, comprehensive COI database from NCBI and BOLD and include customizing options

scripts to parse IrysView output

POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes

Automated chloroplast genome assembly