99 Open source projects that are alternatives of or similar to covid-19-signal

gargammel is an ancient DNA simulator

🚀 A sequencing simulator

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

A package for designing compact and comprehensive capture probe sets.

Remove contaminated contigs from genomes using k-mers and taxonomies.

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

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

A repository for setting up a RNAseq workflow

Cloud-based single-cell copy-number variation analysis tool

Finds SNP sites from a multi-FASTA alignment file

A tool to circularize genome assemblies

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

No description or website provided.

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

Intuitive local web frontend for the BLAST bioinformatics tool

Analysis Pipeline for Single Cell ATAC-seq

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

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

Framework for Metastatic And Clonal History INtegrative Analysis

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

A collection of scripts and notes related to genomics and bioinformatics

Genomics Extension for SQLite

Structural variant toolkit for VCFs

Maximum likelihood demultiplexing

An interactive web tool for quality control of DNA sequencing data

Discovering known and novel miRNAs from small RNA sequencing data

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

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

MaAsLin2: Microbiome Multivariate Association with Linear Models

Meta-Omics Software for Community Analysis

A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.

Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

Analysis pipelines for sequencing data

De novo assembly from Oxford Nanopore reads.

Bonsai: Fast, flexible taxonomic analysis and classification

Rapid large-scale prokaryote pan genome analysis

Contact map analysis for biomolecules; based on MDTraj

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

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

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 robust, extensible metagenomics pipeline

UGENE is free open-source cross-platform bioinformatics software

Collection of scripts for bacterial genomics

Antimicrobial Resistance Identification By Assembly

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

Polyrhythmic Sequencer library for Web Audio API.

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

Multilocus sequence typing by blast using the schemes from PubMLST

Fast in-silico normalization algorithm for NGS data

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

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

From genomes to phenotypes: Traitar, the microbial trait analyzer

Official code repository for GATK versions 4 and up

FASTQ compression

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Deep learning for Metagenome Assembly Error Detection

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).