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

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

GCP Essentials for Bioinformatics Researchers

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

A curated list of awesome Bioinformatics libraries and software.

Code examples of fast and simple k-mer counters for tutorial purposes

Demonstrating best practices for bioinformatics command line tools

Fast multi-line FASTA/Q reader in several programming languages

Genomics Extension for SQLite

A cool place to store your Hi-C

Python module for average nucleotide identity analyses

Bioinformatics Workbook repository

ECG classification programs based on ML/DL methods

SortMeRNA: next-generation sequence filtering and alignment tool

A comprehensive library for computational molecular biology

pymzML - an interface between Python and mzML Mass spectrometry Files

A tool to circularize genome assemblies

✏️ A versatile DNA sequence optimizer

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Race and ethnicity Imputation from Disease history with Deep LEarning

NGLess: NGS with less work

MOLGENIS - for scientific data: management, exploration, integration and analysis.

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Benchmarking programming languages/implementations for common tasks in Bioinformatics

Structural variant toolkit for VCFs

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

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

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:

A Practical and Efficient NCBI Taxonomy Toolkit

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

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.

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

A collection of scripts and notes related to genomics and bioinformatics

Single cell perturbation prediction

Inference of ploidy and heterozygosity structure using whole genome sequencing data

nim wrapper for htslib for parsing genomics data files

Antimicrobial Resistance Identification By Assembly

Application for making ENCODE Blacklists

A DSL for data-driven computational pipelines

parallel fastq-dump wrapper

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

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

Bioinformatics library for .NET

Simple simulation of single-cell RNA sequencing data

A robust and fast clustering method for amplicon-based studies

APBS - software for biomolecular electrostatics and solvation

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

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

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

An efficient FASTQ manipulation suite

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

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

UGENE is free open-source cross-platform bioinformatics software

A curated list of bioinformatics bench-marking papers and resources.

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

Bayesian haplotype-based mutation calling

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.