398 Open source projects that are alternatives of or similar to Parallel Fastq Dump

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

An interactive web tool for quality control of DNA sequencing data

A Practical and Efficient NCBI Taxonomy Toolkit

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

nim wrapper for htslib for parsing genomics data files

The START App: R Shiny Transcriptome Analysis Resource Tool

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.

Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

Single cell perturbation prediction

Global Biotic Interactions provides access to existing species interaction datasets

A collection of scripts and notes related to genomics and bioinformatics

Characterization of Germline variants

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Parser and database to index the terpene profile of different strains of Cannabis from online databases

Application for making ENCODE Blacklists

A tutorial on methods of 16S analysis with QIIME 1

Antimicrobial Resistance Identification By Assembly

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

Simple simulation of single-cell RNA sequencing data

Python Programming for Biologists

A DSL for data-driven computational pipelines

Emperor a tool for the analysis and visualization of large microbial ecology datasets

dna2vec: Consistent vector representations of variable-length k-mers

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

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Lightweight Iterative Gene set Enrichment in R

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Tools and databases for analyzing HLA and VDJ genes.

Bioinformatics library for .NET

Official code repository for GATK versions 4 and up

APBS - software for biomolecular electrostatics and solvation

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

A robust and fast clustering method for amplicon-based studies

Exact Tandem Repeat Finder (not a TRF replacement)

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

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

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

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

An efficient FASTQ manipulation suite

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

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Randomly subsample sequencing reads to a specified coverage

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

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

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

A versatile pairwise aligner for genomic and spliced nucleotide sequences

UGENE is free open-source cross-platform bioinformatics software

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

Structural variant toolkit for VCFs

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

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A comprehensive library for computational molecular biology

ECG classification programs based on ML/DL methods

Python module for average nucleotide identity analyses

GO enrichment with python -- pandas meets networkx