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A tool to extract LOH blocks from VCF, BAM and FASTA data

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment.

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

Quality of life improvements for Bioinformatics in Python.

PyPop: Python for Population Genomics

Genomics_adventure ⭐ 17

Workshop on Genomics - Genomics Adventure

Genomics data re-analysis

High-level API for storing and querying sequence variant data

A long-read analysis toolbox for cancer and population genomics

A Framework to call Structural Variants from NGS based datasets

Ontologies ⭐ 16

Home of the Genomic Feature and Variation Ontology (GFVO)

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

Orthosnap ⭐ 16

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Bioutils ⭐ 16

provides common tools and lookup tables used primarily by the hgvs and uta packages

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

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

Links to data science, bioinformatics, statistics, and machine learning resources

Genoiser ⭐ 16

A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.

Starfish ⭐ 16

starfish: a modular toolkit for giant mobile element annotation

Mapping Iterative Assembler ⭐ 15

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Introme prioritises coding and noncoding splice-altering variants for clinical variant interpretation

Manhattan_generator ⭐ 15

Manhattan plot Generator

Driverpower ⭐ 15

Pytrimal ⭐ 15

Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!

Omicssuite.github.io ⭐ 15

OmicsSuite website for releasing new version.

Covigator Ngs Pipeline ⭐ 15

A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

Bio Tradis ⭐ 15

A set of tools to analyse the output from TraDIS analyses

Python module to read binary Plink files.

Saffrontree ⭐ 14

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

Hicreppy ⭐ 14

Python reimplementation of hicrep with compatibility for sparse matrices

A fast tool for detecting and decomposing segmental duplications in genome assemblies

GMQL - GenoMetric Query Language

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

Identify phage regions in bacterial genomes for masking purposes

Discount ⭐ 14

Very large scale k-mer counting and analysis on Apache Spark.

Nanorepeat ⭐ 13

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

Prophage_tracer ⭐ 13

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

Ruby Minimap2 ⭐ 13

Powerful long read aligner for Ruby

Seven Bridges Genomics aligner/caller debugging and analysis tools

Biobtree ⭐ 13

A bioinformatics tool to search, map and retrieve identifiers, keywords and attributes

Clustassess ⭐ 13

Tools for assessing clustering robustness

MutView is a tool to look the reads cover a mutation in bam file, output file is html format, just like a lightweight IGV(Integrative Genomics Viewer).

Edgecase ⭐ 13

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Mdmcleaner ⭐ 13

MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs

Reference genome quality scores

Genegrouper ⭐ 13

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

Grandeur ⭐ 13

UPHL's Reference Free Pipeline

Query sequence database by HMMs arranged in predefined synteny structure

Chia Pet_tool_v3 ⭐ 13

ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster and visulization

Region Plot ⭐ 12

A tool to plot significant regions of GWAS

1000 Genomes Project Metadata R Package

Analysing Capture Seq Count Data

Faster_lmm_d ⭐ 12

A faster lmm for GWAS. Supports GPU backend.

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

BACNET is a Java based platform to develop website for multi-omics analysis

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling fr

Explore and analyze biological sequence data

Clair3 Trio ⭐ 12

Clair3-Trio: variant calling in trio using Nanopore long-reads

TeraPCA is a multithreaded C++ software suite based on Intel's MKL library (or any other BLAS and/or LAPACK distribution). TeraPCA features no dependencies to external libraries and combines the robustness of subspace iteration with the power of randomization.

바닥부터 시작하는 R + 바이오인포

Secphase ⭐ 12

Phasing reads with secondary alignments

Pymuscle5 ⭐ 12

Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.

Library for indexing VCF files for random access searches by rsID

Genomehubs ⭐ 12

Search and explore genomic metadata, Earth BioGenome Project progress and assembly features

Fontools ⭐ 12

JSON-based FON (Feature Object Notation) format and tools to simplify genomic annotations usage

Automatic evaluation of HGTs

Genomicscourse ⭐ 11

For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics

Deepvariant On Spark ⭐ 11

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

Genomics Workspace ⭐ 11

Django website project for common sequence search tools.

Hicbrowser ⭐ 11

Simple web browser to visualize HiC tracks

Macrosyntr ⭐ 11

R package for comparison of synteny conservation at the genome-wide scale.

[in development] Proof-of-Concept variation translation, validation, and registration service

Lodestone ⭐ 11

Mycobacterial pipeline

HTSlib bindings for Crystal

Genome On Diet ⭐ 11

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

Sequence Database Curator ⭐ 10

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

Polishclr ⭐ 10

A nextflow pipeline for polishing CLR assemblies

Intelligent and cost-effective bidding on cloud computing instances for bioinformatics pipelines.

Readdatastores.jl ⭐ 10

Datastores for reads, not your papa's FASTQ files.

A Boolean Algebra for Genetic Variants

Fraggenescanrs ⭐ 10

Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.

Biochem 3bp3 ⭐ 10

Lectures and Lab Exercises for Biochem 3BP3 Practical Bioinformatics for the Genomics Era

Cazy_webscraper ⭐ 10

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

Bioinformatics Toolbox ⭐ 10

Docker container for bioinformatics tools and pipelines

Fast Bayesian Hidden Markov Model with Wavelet Compression

Positive Selection ⭐ 10

Scripts and procedures for detecting positively selected genes and codons in primates

Bioinformatics ⭐ 10

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

Ngsderive ⭐ 10

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

Please consider using/contributing to https://github.com/nf-core/sarek

Divbrowse ⭐ 10

A web application for interactive visualization and exploratory data analysis of variant call matrices

Whale.jl ⭐ 10

Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation

SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

WorkFlow Package Manager

a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Riboraptor ⭐ 9

Tool for ribo-seq analysis

Python Library for data analysis based on GMQL

Triti Map ⭐ 9

A Snakemake-based pipeline for gene mapping in Triticeae.

Related Searches

Python Bioinformatics (1,492)

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