LisaBlazek

Python4Bioinformatics

Lecture resources for Python for Bioinformatics EANBiT course.

treeCl

Phylogenetic clustering package

training-material

A collection of Galaxy-related training material

revis

raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

angsd

Program for analysing NGS data.

standard-RAxML

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

KmerGO

KmerGO is a user-friendly tool to identify the group-specific sequences on two groups or trait-associated sequences of high throughput sequencing datasets.

mTR

tandem repeat finding from erroneous long reads

TandemTools

Tool for assessing/improving assembly quality in extra-long tandem repeats

ksift

ntHits

Identifying repeats in high-throughput sequencing data

SeqGrapheR

RagTag

Tools for fast and flexible genome assembly scaffolding and improvement

deviaTE

Python tool for the analysis and visualization of mobile genetic elements

DiscoPlot

Visualising discordant reads

figtree

Automatically exported from code.google.com/p/figtree

manticore

A software for the analysis of hybrid genomes through parental NGS data

minigraph

Sequence-to-graph mapper and graph generator

TEMP2

Algorithm to detect germline and de novo transposon insertions

TEMP

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data

jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.

TEFLoN

TEFLoN uses paired-end illumina sequence data to discover and genotype transposable elements present in your samples.

svim-asm

Structural Variant Identification Method using Genome Assemblies

VCF-Simplify

A python parser to simplify and build the VCF (Variant Call Format).

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

VariantVisualization.jl

Julia package powering VIVA, our tool for visualization of genomic variation data. Manual: