505 Open source projects that are alternatives of or similar to SVCollector

C library for high-throughput sequencing data formats

Data intensive science for everyone.

Genotyping of segregating mobile elements insertions

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

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

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

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Java utilities for Bioinformatics

NGLess: NGS with less work

A package for designing compact and comprehensive capture probe sets.

Syntax highlighting for computational biology

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

R package for analyzing single-cell RNA-seq data

A Java API for high-throughput sequencing data (HTS) formats.

Toolset for SV simulation, comparison and filtering

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Scalable genomic data analysis.

Predict plasmids from uncorrected long read data

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

Official code repository for GATK versions 4 and up

UGENE is free open-source cross-platform bioinformatics software

Structural variant toolkit for VCFs

cython + htslib == fast VCF and BCF processing

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

A collection of scripts and notes related to genomics and bioinformatics

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

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

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

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Haplotype VCF comparison tools

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Bayesian genotyper for structural variants

A simplified pipeline for ctDNA sequencing data analysis

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

annotate a VCF with other VCFs/BEDs/tabixed files

Project metadata manager for PEPs in Python

myVCF: a web-based platform for target and exome mutations data management

Tools to process and analyze deep sequencing data.

dysgu-SV is a collection of tools for calling structural variants using short or long reads

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

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

highly-efficient & lightweight mutation signature matrix aggregation

Tools for working with genomic and high throughput sequencing data.

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

WebGL Heatmap Viewer for Big Data and Bioinformatics

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

Streamlining SLAM-seq analysis with ultra-high sensitivity

Complex structural variant detection from WGS data

Improving genome bins through the combination of different binning programs

An R package for reproducible and automated ADMIXTOOLS analyses

Compute N50/NG50 and auN/auNG

Version 5 of the CAFE phylogenetics software

Read and write FASTQ and FASTA efficiently from Python