379 Open source projects that are alternatives of or similar to instaGRAAL

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

find large indels (in the blind spot between GATK/freebayes and SV callers)

A fast tool for hybrid genome assembly of long and short reads

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

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

De novo genome assembly and multisample variant calling

Create Next Stack is a website and CLI tool used to easily set up the boilerplate of new Next.js apps.

Collection of scripts for bacterial genomics

Find target sites for the miRNAs in genomic sequences

🔥 A seed project to help us get up & running with Progressive Web Apps, Google Analytics, Angular Universal, and be able to deploy to App Engine & GitHub Pages

Suite of tools for use in genome assembly and consensus. Work in progress.

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Biopython Jupyter Notebook tutorial to characterize a small genome

xHLA: Fast and accurate HLA typing from short read sequence data

A WGS de novo assembler based on the FMD-index for large genomes

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Finds SNP sites from a multi-FASTA alignment file

Genomics Workflows on AWS

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"

The missing CMake project initializer

simuG: a general-purpose genome simulator

Haplotype VCF comparison tools

A tool for fast and accurate summarizing of variant calling format (VCF) files

ultra simple project scaffolding

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

Genome Annotation Without Nightmares

Seven Bridges Genomics aligner/caller debugging and analysis tools

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

Laravel 5.5+ Front-end preset for UIKit 3.

Phage-Host Interaction Search Tool

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

The GenePattern Server web application

JavaScript VisualizationTools

High-performance error correction for Illumina resequencing data

Official git repository for Biopython (originally converted from CVS)

cython + htslib == fast VCF and BCF processing

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Genome-wide imputation pipeline

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

An ultrafast memory-efficient short read aligner

Easy genetic ancestry predictions in Python

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

Performant Pythonic GenomicRanges

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

A comprehensive Flask boilerplate to build SaaS applications that includes Stripe billing, emails, login, and OAuth.

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

🔬 BEDOPS: high-performance genomic feature operations

Python package and CLI for whole-genome duplication related analyses