961 Open source projects that are alternatives of or similar to saffrontree

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

Assembling the cause of phenotypes and genotypes from NGS data

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

Finds SNP sites from a multi-FASTA alignment file

Multilocus sequence typing by blast using the schemes from PubMLST

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

Predict plasmids from uncorrected long read 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

A tool to circularize genome assemblies

Antimicrobial Resistance Identification By Assembly

Rapid large-scale prokaryote pan genome analysis

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

Official code repository for GATK versions 4 and up

Analysis pipelines for sequencing data

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

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

Intuitive local web frontend for the BLAST bioinformatics tool

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

A package for designing compact and comprehensive capture probe sets.

Data intensive science for everyone.

An interactive web tool for quality control of DNA sequencing data

Bystro genetic analysis (annotation, filtering, statistics)

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

Genomics Extension for SQLite

A collection of scripts and notes related to genomics and bioinformatics

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Code examples of fast and simple k-mer counters for tutorial purposes

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

dysgu-SV is a collection of tools for calling structural variants using short or long reads

NGLess: NGS with less work

Bayesian haplotype-based mutation calling

nim wrapper for htslib for parsing genomics data files

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A cool place to store your Hi-C

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

A curated list of bioinformatics bench-marking papers and resources.

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Reads simulator

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

A repository for setting up a RNAseq workflow

Ten Quick Tips for Deep Learning in Biology

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

GenomeTools genome analysis system.

UGENE is free open-source cross-platform bioinformatics software

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

Deep learning infrastructure for bioinformatics

A genome browser that shows long reads and complex variants better

Toolkit for preparing genomes for submission to NCBI

An ultrafast memory-efficient short read aligner

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

cython + htslib == fast VCF and BCF processing

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

🔬 BEDOPS: high-performance genomic feature operations

Official git repository for Biopython (originally converted from CVS)

JavaScript VisualizationTools

A faster lmm for GWAS. Supports GPU backend.

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

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

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