estolle

JupiterPlot

A Circos-based tool to visualize genome assembly consistency

AGAT

Another Gtf/Gff Analysis Toolkit

fd

A simple, fast and user-friendly alternative to 'find'

biocode

Bioinformatics code libraries and scripts

exonerate-gff3

exonerate fork with added gff3 support

twisst

Topology weighting by iterative sampling of sub-trees

genomics_general

General tools for genomic analyses.

phast

PHAST

CAMSA

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

dnaPipeTE

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

TandemRepeatFinder_scripts

structome

Toolbox development for structural variations within Irys data retrieved from the BioNano Genomics nick-labeling protocols.

sequencetools

Set of scripts etc. to work with DNA sequence and related files

misc

Useful small programs

MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

proteny

A tool to analyze synteny at the protein level.

BNG-FragileSiteRepair

Scripts for repairing (stitching) fragile sites of BioNano genome maps.

fuzzyjoin

Join tables together on inexact matching

sam2pairwise

sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.

AGOUTI

Annotated Genome Optimization Using Transcriptome Information

FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

OrthoFinder

Phylogenetic orthology inference for comparative genomics

flo

Same species annotation lift over pipeline.

Krona

Interactively explore metagenomes and more from a web browser.

ghost-tree

creating hybrid-gene phylogenetic trees for diversity analyses

batalign

wham

Structural variant detection and association testing

newick_utils

shell tools for processing phylogenetic trees

dendroscope3

Dendroscope program for analyzing and visualizing rooted phylogenetic trees and networks