viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://github.com/ctriermaansson/dnafusion
Identification of gene-fusions, including EML4-ALK
cerebra
cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files - Published in JOSS (2020)
https://github.com/broadinstitute/long-read-pipelines
Long read production pipelines
rmetl
rMETL - realignment-based Mobile Element insertion detection Tool for Long read
nrex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
https://github.com/brentp/indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
https://github.com/biodataanalysisgroup/synth4bench
A framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.
nf-platypusindelcalling
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
fair_gatk_mutect2
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
germlineshortv_biovalidation
Workflow for biological validation of germline SNP and indel variant datasets.
vcf-reformatter
🧬 High-performance VCF file parser and reformatter with VEP annotation support. Converts complex VCF files to analyzable TSV format with intelligent transcript handling.
variantbenchmarking
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
https://github.com/cidgoh/nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.
grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.
minmutfinder
Tool written in Python and Bash implemented in a Nextflow pipeline that accurately identifies mutations and assesses their frequencies, accounting for multiple nucleotide mutations occurring within a single codon. Additionally, it can annotate mutations associated to phenotypical changes in viral populations based on user-supplied datasets.
https://github.com/cdcgov/nchhstp-dtbe-varpipe-wgs
This repository contains an analysis pipeline developed to characterize WGS output
pipelines_inmegen
Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.
covid19
SARS-CoV-2 analysis pipeline for short-read, paired-end illumina sequencing
sawfish
Joint structural variant and copy number variant caller for HiFi sequencing data