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indels

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Illumina /manta

Structural variant and indel caller for mapped sequencing data

bioinformatics structural-variations indels structural-variation

UpdatedDec 21, 2022
C++

Illumina /strelka

Strelka2 germline and somatic small variant caller

bioinformatics snps indels snvs

UpdatedDec 29, 2021
C++

walaj /svaba

Structural variation and indel detection by local assembly

c-plus-plus variants structural-variations indels assembled-contigs

UpdatedMar 12, 2025
C++

nygenome /lancet

Microassembly based somatic variant caller for NGS data

cancer-genomics somatic-mutations indels snvs debruijn-graph variant-callers local-assembly

UpdatedJun 23, 2022
C

mozack /abra2

ABRA2

ngs dna rna indels abra splice-junctions realigner

UpdatedDec 2, 2022
Java

bioinformatics-centre /BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers

ngs bayesian-inference variant-calling indels gibbs-sampling structural-variation snvs dna-sequencing genotyping k-mers variant-graphs

UpdatedApr 1, 2019
C++

Illumina /PlatinumGenomes

The Platinum Genomes Truthset

indels variant-analysis snvs

UpdatedNov 8, 2017

HKU-BAL /ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

bioinformatics deep-learning nanopore genomics somatic-variants haplotypes pacbio somatic-mutations illumina indels phasing snvs long-reads ont long-read-sequencing short-reads

UpdatedFeb 27, 2025
Python

sigven /gvanno

Generic human DNA variant annotation pipeline

docker workflow gene singularity vcf variants snv vep disease-gene-association indels annotation-tool vcfanno germline variant-annotations annotation-framework snvs

UpdatedFeb 13, 2024
Python

gear-genomics /indigo

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

sequencing variants alignment crispr-analysis indigo variant-calling pcr indels crispr-cas9 sanger-chromatograms indel-discovery alleles gear-genomics sanger-sequencing pcr-products chromatogram-traces

UpdatedOct 31, 2024
JavaScript

cancerit /dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

somatic-variants ngs snv indels dockstore somatic

UpdatedJun 8, 2020
Shell

aquaskyline /16GT

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

bioinformatics snps genome computational-biology vcf indels call-variants

UpdatedDec 26, 2023
Perl

JosephCrispell /homoplasyFinder

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

consistency mutations indels phylogeny nucleotide-alignment homoplasy

UpdatedJun 2, 2021
R

Sydney-Informatics-Hub /Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

bioinformatics snps genomics nextflow cancer somatic-variants ngs metagenomics bioinformatics-pipeline rnaseq variant-calling transcriptomics indels bioinformatics-analysis bioinformatics-scripts germline-variants research-computing nextflow-pipelines sydney-informatics-hub

UpdatedFeb 28, 2025

swvanderlaan /MetaGWASToolKit

A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies

gwas genome variants meta-analysis indels chromosome association-studies gwas-dataset allele-frequencies allele-counts

UpdatedJan 14, 2025
Shell

ylab-hi /ScanNeo2

Snakemake-based computational workflow for neoantigen prediction from diverse sources

snakemake gene-fusion indels peptide snakemake-workflow splicing epitope neoantigens exitron neoepitope

UpdatedMar 12, 2025
Python

BIMSBbioinfo /crispr_DART

A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data

python r rmarkdown bioconductor crispr-analysis crispr indels snakemake-workflows crispr-cas9

UpdatedFeb 1, 2024
R

adigorla /xgap

xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from next-generation DNA sequencing data.

bioinformatics genomics hpc ngs slurm pipeline-framework sge bioinformatics-pipeline snv indels

UpdatedOct 21, 2020
Python

alexcoppe /iWhale

🐳 Dockerized WES pipeline for variants identification in mathced tumor-normal samples

docker bioinformatics snps genomics biology tumor indels whole-exome-sequencing scons

UpdatedMay 27, 2020
Python

henryjuho /parus_indel

Barton and Zeng (2019) - Pipeline for great tit indel analysis.

genomics selection population-genetics indels dfe

UpdatedApr 8, 2019
Python

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