jbedo Justin Bedő

Utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

Find and characterise transposable element insertions

High-performance read alignment, quantification and mutation discovery

Read aligner for short reads

Genetic variant annotation and effect prediction toolbox

Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files

SAM/BAM processing tool

Python bindings for the LZO data compression library

Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index

Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data

Tools for manipulating biological data, particularly multiple sequence alignments

Python bindings for the LZO data compression library

Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index

Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data

Tools for manipulating biological data, particularly multiple sequence alignments

Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF

Bayesian haplotype-based mutation calling

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Short read genome assembler

Genomic sequence aligner

Collection of optimised low-level functions targeting storage applications

Graph based aligner

Ultra-fast computation of genome mappability

Ultra-fast all-in-one FASTQ preprocessor

Powerful toolset for genome arithmetic

Suite of tools for addressing questions arising in genomics studies