281 Open source projects that are alternatives of or similar to viralrecall

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

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

Provide R access to the NCI Genomic Data Commons portal.

Complex structural variant detection from WGS data

A modular annotation tool for genomic variants

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

An interactive web portal for exploring immuno-oncology data

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

A faster lmm for GWAS. Supports GPU backend.

Bystro genetic analysis (annotation, filtering, statistics)

(WIP) best-practices workflow for rare disease

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

Introduction to Cloud Computing for Genomics

Fast hash function for DNA sequences

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

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

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

PERF is an Exhaustive Repeat Finder

De novo assembly based variant calling pipeline for Illumina short reads

Toolkit for preparing genomes for submission to NCBI

Genetic Map Comparison

My collection of light bioinformatics analysis pipelines for specific tasks

Inference of switch-like differential expression along single-cell trajectories

pythonic wrapper for htslib

Version 2.1.0 released

Compute N50/NG50 and auN/auNG

Clustering scRNAseq by genotypes

An ontology of cell types

A package for designing compact and comprehensive capture probe sets.

A fast 23andMe genome text file parser, now superseded by arv

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

A curated list of awesome bioinformatics software.

echt rapid variant annotation and filtering

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Data Wrangling and Processing for Genomics

Fast alignment and preprocessing of chromatin profiles

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Predict plasmids from uncorrected long read data

Create you virus in termux!

Assembling the cause of phenotypes and genotypes from NGS data

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Malware samples for analysis, researchers, anti-virus and system protection testing.(1300+ Malware-samples!)

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

An open-access bioinformatics text

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

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

A simple command-line tool to download data from Joint Genome Institute databases

Feature Annotation Location Description Ontology

Chanjo provides a better way to analyze coverage data in clinical sequencing.

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

Environmental DNA metabarcoding taxonomic identification

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Find causal cell-types underlying complex trait genetics

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

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

De novo genome assembly and multisample variant calling

Earl Grey: A fully automated TE curation and annotation pipeline

Home of the Genomic Feature and Variation Ontology (GFVO)

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion