291 Open source projects that are alternatives of or similar to LRSDAY

Large genome reassembly based on Hi-C data, continuation of GRAAL

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

Example client programs for Saphetor's VarSome annotation API

Predict plasmids from uncorrected long read data

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

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

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

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

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

Earl Grey: A fully automated TE curation and annotation pipeline

Toolkit for preparing genomes for submission to NCBI

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

De novo genome assembly and multisample variant calling

Genome Annotation Without Nightmares

Official git repository for Biopython (originally converted from CVS)

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

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

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

Phage-Host Interaction Search Tool

Find target sites for the miRNAs in genomic sequences

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

SDK for GPU accelerated genome assembly and analysis

Technology agnostic long read analysis pipeline for transcriptomes

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

JavaScript VisualizationTools

Population assignment analysis using R

cython + htslib == fast VCF and BCF processing

Biopython Jupyter Notebook tutorial to characterize a small genome

An ultrafast memory-efficient short read aligner

Genomics Workflows on AWS

Performant Pythonic GenomicRanges

Finds SNP sites from a multi-FASTA alignment file

🔬 BEDOPS: high-performance genomic feature operations

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

Fast large scale matrix visualization for the web.

simuG: a general-purpose genome simulator

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

Proof-of-concept seq-to-graph mapper and graph generator

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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

Collection of scripts for bacterial genomics

High-performance error correction for Illumina resequencing data

Intuitive local web frontend for the BLAST bioinformatics tool

A powerful open source data warehouse system

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

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

Genome-wide imputation pipeline

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

Chromosome visualization for the web

Deep learning infrastructure for bioinformatics

Seven Bridges Genomics aligner/caller debugging and analysis tools

Ten Quick Tips for Deep Learning in Biology

Reads simulator

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

Easy genetic ancestry predictions in Python

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

Rapid large-scale prokaryote pan genome analysis