35 Open source projects that are alternatives of or similar to PopDel

Complex structural variant detection from WGS data

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

Fast and accurate gene fusion detection from RNA-Seq data

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

simuG: a general-purpose genome simulator

A tool for fast and accurate summarizing of variant calling format (VCF) files

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

xHLA: Fast and accurate HLA typing from short read sequence data

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.

An Efficient Swiss Army Knife for Population Genomic Analyses in R

De novo genome assembly and multisample variant calling

De novo assembly based variant calling pipeline for Illumina short reads

Sentieon DNAseq

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

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.

find large indels (in the blind spot between GATK/freebayes and SV callers)

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

💾 📃 "Reads to report" for public health and clinical microbiology

PEPPER-Margin-DeepVariant

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

Allele-specific copy number estimation with whole genome sequencing

Method to optimally select samples for validation and resequencing

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Identification of segmental duplications in the genome

Tools for processing and analyzing structural variants.

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

The Modular Aligner and The Modular SV Caller

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

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