398 Open source projects that are alternatives of or similar to Sv2

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

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

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

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

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

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

an implementation of NSGA-II in java

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

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

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

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

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

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

Fast & accurate alignment of barcoded short-reads

Official code repository for GATK versions 4 and up

JAMP - Just Another Metabarcoding Pipeline

Randomly subsample sequencing reads to a specified coverage

Data and analysis for the Splatter paper

Lightweight Iterative Gene set Enrichment in R

Data intensive science for everyone.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A plotly.js React component from Plotly 📈

Exact Tandem Repeat Finder (not a TRF replacement)

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

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

Javascript full-stack framework for Big Data visualisation and analysis

List of Computer Science courses with video lectures.

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

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

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

A wrapper for the EnsEMBL REST API

Comprehensive toolkit for generating various numerical features of protein sequences

Analysis pipelines for sequencing data

(formerly eelpond) an automated RNA-Seq workflow system

Snakemake-based workflow for detecting structural variants in WGS data

highly-efficient & lightweight mutation signature matrix aggregation

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

DEPRECIATED! Please use nf-core/tools instead

课题组每周研讨会

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

Yet Another Chimeric Read Detector

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

A lightweight immune repertoire browser

Toolkit for processing sequences in FASTA/Q formats

Create regional association plots from GWAS or meta-analysis

Scalable genomic data analysis.

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

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

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

Unix, R and python tools for genomics and data science

GeneValidator: Identify problems with predicted genes

Estimate metagenomic coverage and sequence diversity

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

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

Tools and databases for analyzing HLA and VDJ genes.

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

🐣 locally query the ncbi taxonomy