⚡ ♒ Rapid prokaryotic genome annotation

Trinity RNA-Seq de novo transcriptome assembly

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

Extensive de-novo TE Annotator

Rapid large-scale prokaryote pan genome analysis

Core BioPerl 1.x code

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.

Convert various sequence formats to FASTA

MITObim - mitochondrial baiting and iterative mapping

simuG: a general-purpose genome simulator

Tools for working with second gen assemblies, fasta sequences, etc

A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.

Tools for the analysis of structural variation in genomes

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

PacBio hybrid error correction through iterative short read consensus

Graph-based mapping of long sequences, noisy or HiFi.

Structural Variants Pipeline for Long Reads

Laboratory Information Management System

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Diamond2GO is a set of tools that can rapidly assign Gene Ontology (GO) terms and perform functional enrichment for large-scale functional genomics datasets.

Workflows I find helpful for fungal genome annotation

Just Annotate My Genome

Genotyping of segregating mobile elements insertions

Combine structural variation outputs from long sequencing reads into a superior call set

Search for activating regulatory variants in the tumor genome

An integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing data

A computational framework for tetrad-based genotyping & recombination landscape analysis

Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina reads