438 Open source projects that are alternatives of or similar to Sambamba

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

annotate a VCF with other VCFs/BEDs/tabixed files

Build and maintain multiple custom conda environments all in once place.

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

Earl Grey: A fully automated TE curation and annotation pipeline

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A fast 23andMe genome text file parser, now superseded by arv

Efficient pythonic random access to fasta subsequences

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

Predict plasmids from uncorrected long read data

A fast and sensitive gapped read aligner

Examples using Clustergrammer2 to explore high-dimensional datasets.

Highly adaptable common interface for proteomics search and de novo engines

VirNet: A deep attention model for viral reads identification

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Cutadapt removes adapter sequences from sequencing reads

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

This library tackles the construction and efficient execution of computational chemistry workflows

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

A library to build and execute typed scientific workflows

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

Fast motif matching in R

Python library to facilitate genome assembly, annotation, and comparative genomics

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

The uncompromising Snakemake code formatter

A curated list of awesome bioinformatics software.

A graphical text editor

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

COBRApy is a package for constraint-based modeling of metabolic networks.

The Ontology for Biomedical Investigations

Read DNA sequences from colourful Microsoft Word documents

SAM: Sharpness-Aware Minimization (PyTorch)

Fast alignment and preprocessing of chromatin profiles

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

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

A simple/sample AngularV4-based web app that demonstrates different API authentication options using Amazon Cognito and API Gateway with an AWS Lambda and Amazon DynamoDB backend that stores user details in a complete end to end Serverless fashion.

A computational library for learning and evaluating biological knowledge graph embeddings

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Welcome to the Innovator Island serverless workshop! This repo contains all the instructions and code you need to complete the workshop. Questions? Contact @jbesw.

Provide R access to the NCI Genomic Data Commons portal.

The Microbiome Interpretable Temporal Rule Engine

Useful bioinformatic scripts

An analysis and visualization platform for 'omics data

My own tools code for NGS data analysis (Next Generation Sequencing)

A simplified pipeline for ctDNA sequencing data analysis

An open-access bioinformatics text

Open-source bioinformatics components for Dash

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.

Phylogenetic trees in Julia

The next version of bwa-mem

A modern genome browser built with JavaScript and HTML5.

Plant image analysis using OpenCV

Java utilities for Bioinformatics