623 Open source projects that are alternatives of or similar to gencore

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

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

Official code repository for GATK versions 4 and up

Data intensive science for everyone.

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

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

UGENE is free open-source cross-platform bioinformatics software

A package for designing compact and comprehensive capture probe sets.

Intuitive local web frontend for the BLAST bioinformatics tool

A simplified pipeline for ctDNA sequencing data analysis

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

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Structural variant toolkit for VCFs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Method to optimally select samples for validation and resequencing

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

C library for high-throughput sequencing data formats

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

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

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

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

Analysis pipelines for sequencing data

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

A collection of scripts and notes related to genomics and bioinformatics

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

NGLess: NGS with less work

R package for analyzing single-cell RNA-seq data

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

Collection of scripts for bacterial genomics

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

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

A tool to circularize genome assemblies

Tools for working with genomic and high throughput sequencing data.

A repository for setting up a RNAseq workflow

Assembling the cause of phenotypes and genotypes from NGS data

Genomics Extension for SQLite

Tools to process and analyze deep sequencing data.

highly-efficient & lightweight mutation signature matrix aggregation

Java utilities for Bioinformatics

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

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

Scalable long read self-correction and assembly polishing with multiple sequence alignment

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Antimicrobial Resistance Identification By Assembly

An interactive web tool for quality control of DNA sequencing data

Rapid large-scale prokaryote pan genome analysis

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Project metadata manager for PEPs in Python

This is my attempt to list all possible blockchain consensus out there, i welcome pull request of the blockchain community! lets make it the main reference for blockchain consensus

Per-base per-nucleotide depth analysis

Genomics data visualization in Python by using matplotlib.

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

A computational library for learning and evaluating biological knowledge graph embeddings

A library to build and execute typed scientific workflows

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Examples using Clustergrammer2 to explore high-dimensional datasets.

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

exploratory and interactive microbiome analyses based on heatmaps

Provide R access to the NCI Genomic Data Commons portal.