423 Open source projects that are alternatives of or similar to Soapdenovo2

Project metadata manager for PEPs in Python

Predict plasmids from uncorrected long read data

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

A curated list of awesome Bioinformatics libraries and software.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Examples using Clustergrammer2 to explore high-dimensional datasets.

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Estimate metagenomic coverage and sequence diversity

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

A library to build and execute typed scientific workflows

Javascript full-stack framework for Big Data visualisation and analysis

APBS - software for biomolecular electrostatics and solvation

A collection of publications on comparison of high-throughput sequencing technologies.

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

React rerelease of MSAViewer

Genotyping of segregating mobile elements insertions

Structural variant toolkit for VCFs

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

A wrapper for the EnsEMBL REST API

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.

Genome annotation with AUGUSTUS

Per-base per-nucleotide depth analysis

Genomics data visualization in Python by using matplotlib.

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

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

(formerly eelpond) an automated RNA-Seq workflow system

Assembling the cause of phenotypes and genotypes from NGS data

An efficient FASTQ manipulation suite

Stacked Denoising AutoEncoder based on TensorFlow

highly-efficient & lightweight mutation signature matrix aggregation

GWAS summary statistics files QC tool

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

Rapid determination of appropriate reference genomes.

DEPRECIATED! Please use nf-core/tools instead

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

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

3D printed sculpture of a DNA molecule, showing my own genome

A Python package for fast operations on 1-dimensional genomic signal tracks

Bystro genetic analysis (annotation, filtering, statistics)

Bayesian genotyper for structural variants

A Python platform for Structural Bioinformatics

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

Method to optimally select samples for validation and resequencing

UGENE is free open-source cross-platform bioinformatics software

Toolkit for processing sequences in FASTA/Q formats

VirNet: A deep attention model for viral reads identification

Compute N50/NG50 and auN/auNG

Biological sequences for the julia language

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

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

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Single-Cell Analysis in Python. Scales to >1M cells.

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Scalable genomic data analysis.

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.