415 Open source projects that are alternatives of or similar to sample-sheet

🔬 Assemble large genomes using short reads

Intuitive local web frontend for the BLAST bioinformatics tool

Structural variation caller using third generation sequencing

Examples of using deep learning in Bioinformatics

A genome browser that shows long reads and complex variants better

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

A curated list of resources for learning bioinformatics.

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

RAxML Next Generation: faster, easier-to-use and more flexible

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Quickly search, compare, and analyze genomic and metagenomic data sets.

Toolset for SV simulation, comparison and filtering

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

The Ensembl Compara Perl API and SQL schema

React component for Cytoscape.js network visualisations

ClearML Server for Kubernetes Clusters Using Helm

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

Toolkit for preparing genomes for submission to NCBI

Python package for graph neural networks in chemistry and biology

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Nanopore demultiplexing, QC and alignment pipeline

Deep learning infrastructure for bioinformatics

Core BioPerl 1.x code

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Ten Quick Tips for Deep Learning in Biology

Maximum likelihood demultiplexing

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

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

Remote protein homology detection suite.

No description or website provided.

An ultrafast memory-efficient short read aligner

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

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

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

🔬 BEDOPS: high-performance genomic feature operations

A faster lmm for GWAS. Supports GPU backend.

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

code for reading and processing Allen Institute for Brain Science data

Genomics using open source tools, running on GCP or AWS

A powerful open source data warehouse system

Haplotype VCF comparison tools

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

Aligns short reads using dynamic seed size with strobemers

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

A curated list of Cheminformatics libraries and software.

GenomeTools genome analysis system.

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

Protein Graph Library

Official git repository for Biopython (originally converted from CVS)

Python for Bioinformatics

Command line utility for manipulating Illumina-generated FastQ files.

cython + htslib == fast VCF and BCF processing

GNparser normalises scientific names and extracts their semantic elements.

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

Computational Analysis of Novel Drug Opportunities

An accurate and ultra-fast hybrid genome assembler

Strelka2 germline and somatic small variant caller