600 Open source projects that are alternatives of or similar to Awesome Sequencing Tech Papers

Fast motif matching in R

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

List of Computer Science courses with video lectures.

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Accurate sample inference from amplicon data with single nucleotide resolution

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Home of the Genomic Feature and Variation Ontology (GFVO)

A wrapper for the EnsEMBL REST API

Robust, flexible and resource-efficient pipelines using Go and the commandline

Bioinformatics containers

Sample search by metadata and features

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

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

An ontology of cell types

A library for manipulating bioinformatics sequencing formats in Apache Spark

An analysis and visualization platform for 'omics data

Introduction to Cloud Computing for Genomics

Maximum likelihood demultiplexing

Genotyping of segregating mobile elements insertions

Explore gnomAD datasets on the web

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

Ultrafast sequence typing and gene detection from NGS raw reads

A D library for computational biology and bioinformatics

Feature extraction algorithm for genomic data

an implementation of NSGA-II in java

Analysing Capture Seq Count Data

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

🎯 Human transcription factor target genes.

A cross-platform command-line tool for executing jobs in parallel

WebLogo 3: Sequence Logos redrawn

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Per-base per-nucleotide depth analysis

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

Genomics data visualization in Python by using matplotlib.

simple viewer for variant call format using htslib

Ploidy agnostic phasing pipeline and algorithm

A secure encryption tool for genomic data

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Large genome reassembly based on Hi-C data, continuation of GRAAL

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

The GenePattern Server web application

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

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

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Python library to handle Gene Ontology (GO) terms

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

Complex structural variant detection from WGS data

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

Stacked Denoising AutoEncoder based on TensorFlow

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Simple & Efficient data access for Scala and Scala.js

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

Read and write FASTQ and FASTA efficiently from Python

C++ library and cmdline tools for parsing and manipulating VCF files

Fast and accurate sequence demultiplexing

API for linked biological knowledge

echt rapid variant annotation and filtering