194 Open source projects that are alternatives of or similar to bin

A DNA Sequence Alignment/Map (SAM) library for Clojure

Fast and accurate sequence demultiplexing

Frequently used commands in bioinformatics

A D library for computational biology and bioinformatics

Bioinformatics library in Kotlin

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Simple FASTQ quality assessment using Python

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

Simple pure Python SAM parser and objects for working with SAM records

Efficient handling of FASTQ files from Python

Exome/Capture/RNASeq Pipeline Implementation using snakemake

C library for high-throughput sequencing data formats

Syntax highlighting for computational biology

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

A simple tool to calculate reads number and total base count in FASTQ file

pythonic wrapper for htslib

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

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

A collection of Galaxy-related training material

A template for an AWS SAM project with continuous integration.

RNA-seq workflow using STAR and DESeq2

NGLess: NGS with less work

An automated RNA-seq pipeline using Nextflow

This project is developed to help developers add filtering support to their graphql-java services

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

A method for variant graph genotyping based on exact alignment of k-mers

Tools for working with genomic and high throughput sequencing data.

This project is an example about lambda, SAM, dynamodb. This repository contains source code and supporting files for a serverless application that you can deploy with the SAM CLI. It includes the following files and folders.

R package for analyzing single-cell RNA-seq data

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

UGENE is free open-source cross-platform bioinformatics software

A tool to backup and restore AWS Connect, with some useful other utilities too

Sequana: a set of Snakemake NGS pipelines

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Action to set up AWS SAM CLI and add it to the PATH

ABRA2

An easy-to-use way for running Galaxy workflows.

Official code repository for GATK versions 4 and up

C++ Implementation of Savitzky-Golay filtering based on Gram polynomials

A Visual Effects pipeline to manage jobs, shots and software assignment, with a simple asset manager. Its extensively integrated with CortexVFX and Gaffer. (and it builds booth, with support for Maya, Houdini and Nuke, if you have then installed!)

Integration that displays the next event of an ics link (support reoccuring events)

A workflow for creating small NGS test data sets, useful for continuous integration.

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

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Rare variant test software for next generation sequencing data

Transposon Insertion Finder - Detection of new insertions in NGS data

(No maintenance) Detect gene fusion directly from raw fastq files

Java SDK for downloading large gzipped (tsv) item feed files and applying filters for curation

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

A robust model for quantitative comparison of ChIP-Seq data sets.

Estimation of pairwise distances under a probabilistic framework

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Data intensive science for everyone.

Provides unified search model for Yii ActiveRecord

A filtering SOCKS proxy server and client library written in nim.

Tools to process and analyze deep sequencing data.