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

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

EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.

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

Benchmarking programming languages/implementations for common tasks in Bioinformatics

JAMP - Just Another Metabarcoding Pipeline

Bayesian genotyper for structural variants

an implementation of NSGA-II in java

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

Data and analysis for the Splatter paper

Biological sequences for the julia language

A robust model for quantitative comparison of ChIP-Seq data sets.

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

Data intensive science for everyone.

An interactive web tool for quality control of DNA sequencing data

Aggregate results from bioinformatics analyses across many samples into a single report.

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 plotly.js React component from Plotly 📈

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

Python and C++ code for reading and writing genomics data.

A Practical and Efficient NCBI Taxonomy Toolkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

The START App: R Shiny Transcriptome Analysis Resource Tool

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

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

C library for high-throughput sequencing data formats

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

Biostar Q&A

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.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Global Biotic Interactions provides access to existing species interaction datasets

Versatile open-source tool for microbiome analysis

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

Workflow Description Language - Specification and Implementations

Characterization of Germline variants

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

A collection of scripts and notes related to genomics and bioinformatics

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

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

The next version of bwa-mem

Single cell perturbation prediction

A modern genome browser built with JavaScript and HTML5.

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

Signal-level algorithms for MinION data

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

A tutorial on methods of 16S analysis with QIIME 1

Cutadapt removes adapter sequences from sequencing reads

nim wrapper for htslib for parsing genomics data files

Working with molecular structures in pandas DataFrames

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

Java utilities for Bioinformatics

Antimicrobial Resistance Identification By Assembly

Python Programming for Biologists

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.

SquiggleKit: A toolkit for manipulating nanopore signal data

A wrapper for the EnsEMBL REST API