398 Open source projects that are alternatives of or similar to Strelka

Exact Tandem Repeat Finder (not a TRF replacement)

Read DNA sequences from colourful Microsoft Word documents

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

Fast alignment and preprocessing of chromatin profiles

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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

An efficient FASTQ manipulation suite

A computational library for learning and evaluating biological knowledge graph embeddings

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

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

Examples of using deep learning in Bioinformatics

Provide R access to the NCI Genomic Data Commons portal.

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Useful bioinformatic scripts

UGENE is free open-source cross-platform bioinformatics software

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

Randomly subsample sequencing reads to a specified coverage

An open-access bioinformatics text

Syntax highlighting for computational biology

Unsupervised domain adaptation method for relation extraction

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

Fast and flexible ORF finder

Benchmarking programming languages/implementations for common tasks in Bioinformatics

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Method to optimally select samples for validation and resequencing

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

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

UNCURL is a tool for single cell RNA-seq data analysis.

Compute N50/NG50 and auN/auNG

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

A full spaCy pipeline and models for scientific/biomedical documents.

WebGL Heatmap Viewer for Big Data and Bioinformatics

The sources of the openSNP website

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

🐣 locally query the ncbi taxonomy

A package for designing compact and comprehensive capture probe sets.

A Practical and Efficient NCBI Taxonomy Toolkit

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

React component for Cytoscape.js network visualisations

Read and write FASTQ and FASTA efficiently from Python

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Fast hash function for DNA sequences

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Fast & accurate alignment of barcoded short-reads

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

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

(No maintenance) Detect gene fusion directly from raw fastq files

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

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

An ultrafast memory-efficient short read aligner

code for reading and processing Allen Institute for Brain Science data

Genome assembly evaluation tool

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests