tools for working with genome variation graphs

Variant selection framework in genome graphs

The complete sequence of a human genome

Data and analysis for NA12878 genome on nanopore

Human Pangenome Reference Consortium - HG002 Data Freeze (v1.0)

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Correcting errors in noisy long reads using variation graphs

Optimal sequence-to-graph alignment with recombinations

Network construction, analysis, and comparison for microbial compositional data

IGV Web App

Windowed Adaptive Trimming for fastq files using quality

Supplementary files for my book, "Bioinformatics Data Skills"

Nextflow pipeline for Mutect2 somatic variant calling best practices

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

This repository contains the burrow-wheelr's transform algorithm along with its implementation

Kraken taxonomic sequence classification system

A tool for generating consensus long-read assemblies for bacterial genomes

hybrid assembly pipeline for bacterial genomes

Nanopore data assembler

Fast and accurate de novo assembler for long reads

De novo assembler for single molecule sequencing reads using repeat graphs

A single molecule sequence assembler for genomes large and small.

Toolkit for processing sequences in FASTA/Q formats

Filtering and trimming of long read sequencing data

Quality control for MinION sequencing data

Plotting scripts for long read sequencing data

A Java API for high-throughput sequencing data (HTS) formats.

C library for high-throughput sequencing data formats

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

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