indels

There are 2 repositories under indels topic.

Illumina / manta
Structural variant and indel caller for mapped sequencing data
bioinformatics indels structural-variation structural-variations
Language:C++ 391
Illumina / strelka
Strelka2 germline and somatic small variant caller
bioinformatics snvs indels snps
Language:C++ 350
walaj / svaba
Structural variation and indel detection by local assembly
indels variants assembled-contigs structural-variations c-plus-plus
Language:C++ 227
nygenome / lancet
Microassembly based somatic variant caller for NGS data
somatic-mutations cancer-genomics variant-callers debruijn-graph snvs indels local-assembly
Language:C 153
mozack / abra2
ABRA2
splice-junctions indels dna rna realigner ngs abra
Language:Java 90
bioinformatics-centre / BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
variant-calling genotyping ngs variant-graphs dna-sequencing snvs indels structural-variation bayesian-inference gibbs-sampling k-mers
Language:C++ 86
Illumina / PlatinumGenomes
The Platinum Genomes Truthset
indels snvs variant-analysis
84
HKU-BAL / ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
deep-learning long-reads nanopore ont somatic-mutations somatic-variants bioinformatics genomics haplotypes phasing snvs indels illumina long-read-sequencing short-reads pacbio
Language:Python 65
sigven / gvanno
Generic human DNA variant annotation pipeline
docker gene vep vcfanno germline variant-annotations vcf snv indels annotation-framework annotation-tool workflow singularity snvs variants disease-gene-association
Language:Python 53
gear-genomics / indigo
Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
indels crispr-cas9 crispr-analysis alignment sequencing sanger-chromatograms indel-discovery indigo pcr gear-genomics pcr-products chromatogram-traces sanger-sequencing alleles variant-calling variants
Language:JavaScript 31
cancerit / dockstore-cgpwgs
Dockstore implementation of CGP core WGS analysis
dockstore ngs somatic somatic-variants snv indels
Language:Shell 28
aquaskyline / 16GT
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
call-variants genome vcf indels snps bioinformatics computational-biology
Language:Perl 27
JosephCrispell / homoplasyFinder
A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
phylogeny indels nucleotide-alignment consistency mutations homoplasy
Language:R 19
swvanderlaan / MetaGWASToolKit
A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies
meta-analysis gwas gwas-dataset allele-frequencies variants indels genome association-studies chromosome allele-counts
Language:Shell 13
Sydney-Informatics-Hub / Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis sydney-informatics-hub research-computing germline-variants somatic-variants cancer genomics indels metagenomics ngs rnaseq snps transcriptomics variant-calling nextflow nextflow-pipelines
11
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.
ngs snv indels bioinformatics-pipeline bioinformatics genomics hpc slurm sge pipeline-framework
Language:Python 10
BIMSBbioinfo / crispr_DART
A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data
crispr-analysis indels snakemake-workflows crispr crispr-cas9 rmarkdown bioconductor r python
Language:R 10
ylab-hi / ScanNeo2
Snakemake-based computational workflow for neoantigen prediction from diverse sources
epitope gene-fusion indels neoantigens peptide snakemake snakemake-workflow splicing exitron neoepitope
Language:Python 10
alexcoppe / iWhale
:whale: Dockerized WES pipeline for variants identification in mathced tumor-normal samples
bioinformatics tumor whole-exome-sequencing docker snps indels scons biology genomics
Language:Python 9
henryjuho / parus_indel
Barton and Zeng (2019) - Pipeline for great tit indel analysis.
population-genetics dfe indels genomics selection
Language:Python 7
baezortega / somatypus
A Platypus-based variant calling pipeline for cancer data
variants cancer-data pipeline somatic-variants indels
Language:Python 6
DKFZ-ODCF / IndelCallingWorkflow
A Platypus-based workflow for indel calling
cancer-genomics indels platypus roddy somatic-indels somatic-variants workflow
Language:Python 5
babinyurii / crispr_cas9
NGS data analysis scripts for HBV elimination research group
ngs-analysis virology dna-sequences indels python3 bioinformatics crispr-cas9 deep-sequencing
Language:Python 4
Hanryi / MarkerTech
An advanced genotyping pipeline by next-generation sequencing (NGS) technology
python pipeline genomics genotyping-by-sequencing snps indels
Language:Python 4
henryjuho / drosophila_indels
Barton and Zeng (2018) - Pipeline and scripts for popgen analysis of whole-genome drosophila data.
population-genetics bioinformatics indels insertion deletion drosophila
Language:Python 4
hongenxu / MDV_proj
Scripts used in MDV project
perl snvs indels marek-disease
Language:Perl 4
RhettRautsaw / VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
bcftools gatk gatk-bestpractices indels phasing samtools snps variant-calling
Language:Python 4
alexdonath / gappy2
gappy2 is the successor of gappy v1
splids indels split-inducing-indels gaps alignment
Language:Python 3
cancerit / dockstore-cgpwxs
Dockstore implementation of CGP core WXS analysis
dockstore ngs snv indels
Language:Shell 3
CERC-Genomic-Medicine / WEGS_pipelines
Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.
gatk genetics indels sequencing snps snvs wegs wes wgs
Language:Nextflow 3
albamalagon / FinalDegreeProject
machinelearning genomics snps indels ngsvariants cnvs randomforest decisiontrees ann
Language:Python 2
rki-mf1 / cievad
A tool suite for a simple, streamlined and rapid evaluation of variant callsets
benchmarking bioinformatics genomics indels nextflow ngs oxford-nanopore snps variant-calling
Language:Nextflow 2
HGSC-NGSI / xatlas
Fast and accurate single sample SNV caller
ngs ngs-analysis snp indels bioinformatics
Language:C++ 1
laurentnoe / storm
Illumina (and SOLiD) sensitive read mapping tool (cloned from svn://scm.gforge.inria.fr/svnroot/storm/, original code from @marta- , with some work done by @yoann-dufresne)
read-mapping illumina-sequencing spaced-seed simd-intrinsics openmp-parallelization sequence-alignment fasta fastq fasta-format fastq-format incremental indels sam-output sam-file illumina
Language:C 1
shane-e945 / MitoMut
MitoMut is a tool to call mitochondrial deletions from next generation sequencing (NGS) data
bioinformatics bioinformatics-pipeline indels indel-finder mitochondria python research
Language:Python 1
acg-team / single-char-indel-ASR-preserves-long-indels
This repository includes the scripts used for analysis investigating the dynamics of indels in mammalian orthologous proteins and the examination of the ancestral reconstruction of multiple-character indels under the PIP.
ancestral-sequence-reconstruction indels
Language:Jupyter Notebook

indels

Illumina / manta

Illumina / strelka

walaj / svaba

nygenome / lancet

mozack / abra2

bioinformatics-centre / BayesTyper

Illumina / PlatinumGenomes

HKU-BAL / ClairS

sigven / gvanno

gear-genomics / indigo

cancerit / dockstore-cgpwgs

aquaskyline / 16GT

JosephCrispell / homoplasyFinder

swvanderlaan / MetaGWASToolKit

Sydney-Informatics-Hub / Bioinformatics

adigorla / xgap

BIMSBbioinfo / crispr_DART

ylab-hi / ScanNeo2

alexcoppe / iWhale

henryjuho / parus_indel

baezortega / somatypus

DKFZ-ODCF / IndelCallingWorkflow

babinyurii / crispr_cas9

Hanryi / MarkerTech

henryjuho / drosophila_indels

hongenxu / MDV_proj

RhettRautsaw / VariantCaller

alexdonath / gappy2

cancerit / dockstore-cgpwxs

CERC-Genomic-Medicine / WEGS_pipelines

albamalagon / FinalDegreeProject

rki-mf1 / cievad

HGSC-NGSI / xatlas

laurentnoe / storm

shane-e945 / MitoMut

acg-team / single-char-indel-ASR-preserves-long-indels