336 Open source projects that are alternatives of or similar to open-cravat

echt rapid variant annotation and filtering

Predict plasmids from uncorrected long read data

Multilocus sequence typing by blast using the schemes from PubMLST

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

Assembling the cause of phenotypes and genotypes from NGS data

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

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.

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

Bystro genetic analysis (annotation, filtering, statistics)

simuG: a general-purpose genome simulator

Improve the quality of a denovo assembly by scaffolding and gap filling

Finds SNP sites from a multi-FASTA alignment file

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

A phenotype-based tool for variant prioritization in WES and WGS data

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

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

A tool to plot significant regions of GWAS

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

Interactive assembly and analysis of RAD-seq data sets

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Command line utility for manipulating Illumina-generated FastQ files.

Grammar of Scalable Linked Interactive Nucleotide Graphics

Python toolkit for building restartable pipelines

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

Genomic VCF to tab-separated values

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Use this tool to label forms, bounding boxes, and assigning types to annotations

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

Resource of human chromosome schematics & images

mgatk: mitochondrial genome analysis toolkit

A fast, scalable, and accurate local ancestry method.

🔥 One of the most comprehensive open-source data annotation platform.

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

simple rule based named entity recognition

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Annotation of VCF variants with functional impact and from databases (executable+library)

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Python module for data scientists for quick creating annotation projects.

One-click image sorting/labelling script

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

pythonic wrapper for htslib

Bounding Box Editor and Exporter

🐳 Bio-dockers: dockerized bioinformatic tools

GREIN : GEO RNA-seq Experiments Interactive Navigator

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

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

An R framework for phylostratigraphy

Numerical Encoding for Human Genetic Variants

Identify phage regions in bacterial genomes for masking purposes

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

A bioinformatics pipeline to analyze mtDNA from NGS data

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

Clustering scRNAseq by genotypes

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Tools for analyzing 10X Genomics data

Spark VCF data source implementation for Dataframes

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

A package for designing activity-informed nucleic acid diagnostics for viruses.

WebAssembly modules for genomics