473 Open source projects that are alternatives of or similar to Helmsman

A collection of scripts and notes related to genomics and bioinformatics

Structural variant toolkit for VCFs

C library for high-throughput sequencing data formats

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Bayesian genotyper for structural variants

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Genomics Extension for SQLite

Scalable genomic data analysis.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Syntax highlighting for computational biology

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

cython + htslib == fast VCF and BCF processing

A package for designing compact and comprehensive capture probe sets.

UGENE is free open-source cross-platform bioinformatics software

Intuitive local web frontend for the BLAST bioinformatics tool

Antimicrobial Resistance Identification By Assembly

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Analysis pipelines for sequencing data

A collection of publications on comparison of high-throughput sequencing technologies.

A tool to circularize genome assemblies

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Toolset for SV simulation, comparison and filtering

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Assembling the cause of phenotypes and genotypes from NGS data

Genotyping of segregating mobile elements insertions

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

An interactive web tool for quality control of DNA sequencing data

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Official code repository for GATK versions 4 and up

A repository for setting up a RNAseq workflow

Rapid large-scale prokaryote pan genome analysis

Method to optimally select samples for validation and resequencing

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

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

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Haplotype VCF comparison tools

annotate a VCF with other VCFs/BEDs/tabixed files

Data intensive science for everyone.

A cross-platform command-line tool for executing jobs in parallel

Unix, R and python tools for genomics and data science

Tools for working with SAM/BAM data

The next version of bwa-mem

Toolkit for processing sequences in FASTA/Q formats

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Python library to facilitate genome assembly, annotation, and comparative genomics

A modern genome browser built with JavaScript and HTML5.

List of Computer Science courses with video lectures.

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

A Python package for fast operations on 1-dimensional genomic signal tracks

Aggregate results from bioinformatics analyses across many samples into a single report.

A fast and sensitive gapped read aligner

Signal-level algorithms for MinION data

Plant image analysis using OpenCV

Scripts to download genomes from the NCBI FTP servers

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

Ultra-fast and memory-efficient (meta-)genome assembler

Biostar Q&A

Cutadapt removes adapter sequences from sequencing reads