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Lecture resources for Python for Bioinformatics EANBiT course.
A collection of Galaxy-related training material
RAxML Next Generation: faster, easier-to-use and more flexible
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 H…
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
KmerGO is a user-friendly tool to identify the group-specific sequences on two groups or trait-associated sequences of high throughput sequencing datasets.
Tool for assessing/improving assembly quality in extra-long tandem repeats
Tools for fast and flexible genome assembly scaffolding and improvement
Python tool for the analysis and visualization of mobile genetic elements
Automatically exported from code.google.com/p/figtree
A software for the analysis of hybrid genomes through parental NGS data
Algorithm to detect germline and de novo transposon insertions
TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data
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 uses paired-end illumina sequence data to discover and genotype transposable elements present in your samples.
Structural Variant Identification Method using Genome Assemblies
A python parser to simplify and build the VCF (Variant Call Format).
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Julia package powering VIVA, our tool for visualization of genomic variation data. Manual: