Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

A structural variation pipeline for short-read sequencing

CLI for interacting with Cromwell servers

Segmented HAPlotype Estimation and Imputation Tool

Evaluation of phasing performance

Linked-Reads Community Challenge

10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling

Implementation of Positional Burrows-Wheeler Transform for genetic data

Fast & accurate alignment of barcoded short-reads

software tools for haplotype assembly from sequence data

Genome-wide reconstruction of complex structural variants

heuristics to merge structural variant calls in VCF format.

Tools for 10X

Approach to identify simple and complex structural genomic rearrangements using a randomized approach

Simple R script for plotting ideograms and annotating with bed files.

C library for high-throughput sequencing data formats

Tools (written in C using htslib) for manipulating next-generation sequencing data

Official git repository for Biopython (originally converted from CVS)

DO NOT FORK! This repository is outdated. It is only kept as a reference for old forks. Create a clean clone from https://github.com/biojava/biojava

Scripts for various projects

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link belo…

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential f…