nf-core/raredisease

Call and score variants from WGS/WES of rare disease patients.

Language: Nextflow - Size: 11.1 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 72 - Forks: 33

andersen-lab/ivar Fork of gkarthik/ivar

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

Language: C++ - Size: 15.9 MB - Last synced: about 3 hours ago - Pushed: about 22 hours ago - Stars: 115 - Forks: 38

brentp/indelope

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

Language: Nim - Size: 133 KB - Last synced: about 17 hours ago - Pushed: over 6 years ago - Stars: 39 - Forks: 1

NCI-CGR/GEMSCAN

Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

Language: Python - Size: 17.4 MB - Last synced: about 6 hours ago - Pushed: about 19 hours ago - Stars: 5 - Forks: 7

cidgoh/nf-ncov-voc

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.

Language: Python - Size: 15.2 MB - Last synced: 23 minutes ago - Pushed: about 20 hours ago - Stars: 4 - Forks: 4

vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Language: C++ - Size: 32.9 MB - Last synced: about 20 hours ago - Pushed: 4 days ago - Stars: 596 - Forks: 218

ghga-de/nf-platypusindelcalling

This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ

Language: Python - Size: 119 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

nf-core/variantbenchmarking

A nextflow variant benchmarking pipeline - premature

Language: Nextflow - Size: 2.63 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 4 - Forks: 6

pdimens/harpy

Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.

Language: Python - Size: 385 MB - Last synced: about 7 hours ago - Pushed: 1 day ago - Stars: 9 - Forks: 1

tanghaibao/jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

Language: Python - Size: 9.35 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 692 - Forks: 179

INMEGEN/Pipelines_INMEGEN

Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.

Language: Nextflow - Size: 2.16 MB - Last synced: about 3 hours ago - Pushed: 2 days ago - Stars: 7 - Forks: 0

HKU-BAL/Clair3

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

Language: Python - Size: 3.19 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 218 - Forks: 26

tobiasrausch/nRex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

Language: Shell - Size: 1.85 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 11 - Forks: 1

allytrope/variant-analysis

A Snakemake pipeline for variant calling of genomic FASTQ data using GATK

Language: Python - Size: 2.06 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 5 - Forks: 0

lh3/minipileup

Simple pileup-based variant caller

Language: C - Size: 93.8 KB - Last synced: about 4 hours ago - Pushed: about 1 month ago - Stars: 76 - Forks: 3

iliapopov17/BI-Workshop-miniProjects

Repository for workshop study projects in Bioinformatics Institute 2023-2024

Language: Jupyter Notebook - Size: 16.1 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

alipirani88/snpkit

Modular workflow for Microbial Variant Calling and SNP diagnostics.

Language: Python - Size: 61.8 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 4 - Forks: 4

sanjaynagi/rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Language: Jupyter Notebook - Size: 99.6 MB - Last synced: 2 days ago - Pushed: 6 days ago - Stars: 17 - Forks: 6

HKU-BAL/ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Language: Python - Size: 1.93 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 29 - Forks: 2

GenomicsDB/GenomicsDB

High performance data storage for importing, querying and transforming variants.

Language: C++ - Size: 65.9 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 89 - Forks: 18

nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Language: Nextflow - Size: 82.4 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 333 - Forks: 370

tjiangHIT/rMETL

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

Language: Python - Size: 1.02 MB - Last synced: 7 days ago - Pushed: 8 months ago - Stars: 15 - Forks: 3

solida-core/diva

DiVA (DNA Variant Analysis) is a pipeline for Next-Generation Sequencing Exome data anlysis

Language: Python - Size: 508 KB - Last synced: 9 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 6

maurya-anand/liftover

Convert genomic coordinates from the Human Genome version 19 (hg19) to version 38 (hg38)

Language: Python - Size: 26.4 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

nanoporetech/megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

Language: Python - Size: 24.9 MB - Last synced: 8 days ago - Pushed: 12 months ago - Stars: 189 - Forks: 29

nf-core/viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

Language: Nextflow - Size: 9.78 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 107 - Forks: 95

BCCDC-PHL/alignment-variants

Pipeline to perform alignment & variant calling on whole-genome sequence data

Language: Nextflow - Size: 3.13 MB - Last synced: 13 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

HKU-BAL/Clair3-RNA

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Language: Python - Size: 327 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 7 - Forks: 0

kcleal/dysgu

Toolkit for calling structural variants using short or long reads

Language: Cython - Size: 46.3 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 85 - Forks: 10

anand-imcm/get-variant-info

A WDL-based workflow for extraction of variants and their associated info from large VCF files

Language: Python - Size: 56.6 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

tdayris/fair_gatk_mutect2

Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2

Language: Python - Size: 72.3 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

sequana/sequana

Sequana: a set of Snakemake NGS pipelines

Language: Jupyter Notebook - Size: 35.5 MB - Last synced: 13 days ago - Pushed: about 2 months ago - Stars: 140 - Forks: 27

Sydney-Informatics-Hub/GermlineShortV_biovalidation

Workflow for biological validation of germline SNP and indel variant datasets.

Language: Shell - Size: 143 KB - Last synced: 16 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

IKIM-Essen/uncovar

Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

Language: Python - Size: 3.83 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 20 - Forks: 4

HKU-BAL/Clair3-Trio

Clair3-Trio: variant calling in trio using Nanopore long-reads

Language: Python - Size: 2.74 MB - Last synced: 20 days ago - Pushed: 22 days ago - Stars: 12 - Forks: 1

Clinical-Genomics/BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Language: Python - Size: 228 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 43 - Forks: 16

TileDB-Inc/TileDB-VCF

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

Language: C++ - Size: 33 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 79 - Forks: 13

oicr-gsi/starFusion

Workflow that takes a fastq pair or optionally a chimeric file from STAR and detects RNA-seq fusion events.

Language: WDL - Size: 20.3 MB - Last synced: 18 days ago - Pushed: 10 months ago - Stars: 0 - Forks: 1

oicr-gsi/sample-fingerprinting

workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

Language: wdl - Size: 1.18 MB - Last synced: 18 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 2

gear-genomics/tracy

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

Language: C++ - Size: 3.17 MB - Last synced: 18 days ago - Pushed: about 1 month ago - Stars: 94 - Forks: 19

CRG-CNAG/CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

Language: Nextflow - Size: 29 MB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 129 - Forks: 52

aprilweilab/picovcf

Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.

Language: C++ - Size: 151 KB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 6 - Forks: 0

mbhall88/NanoVarBench

Evaluating Nanopore-based bacterial variant calling

Language: Python - Size: 34.6 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 4 - Forks: 0

dmnfarrell/snipgenie

command line and desktop tool for microbial variant calling

Language: Jupyter Notebook - Size: 122 MB - Last synced: 1 day ago - Pushed: 17 days ago - Stars: 8 - Forks: 0

kishwarshafin/pepper

PEPPER-Margin-DeepVariant

Language: Python - Size: 36.1 MB - Last synced: 29 days ago - Pushed: 4 months ago - Stars: 230 - Forks: 42

SUwonglab/arcsv

Complex structural variant detection from WGS data

Language: Python - Size: 5.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 20 - Forks: 6

sablokgaurav/bcftools-filter

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

Language: Python - Size: 157 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

moiexpositoalonsolab/grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

Language: Python - Size: 93.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 78 - Forks: 18

bioinf/RMAhunter

Language: HTML - Size: 116 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 7 - Forks: 0

LorenaDerezanin/pipeline_test

Variant calling pipeline (Snakemake workflow)

Language: Python - Size: 1.14 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

broadinstitute/long-read-pipelines

Long read production pipelines

Language: Jupyter Notebook - Size: 179 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 111 - Forks: 22

TimD1/vcfdist

vcfdist: Accurately benchmarking phased variant calls

Language: C++ - Size: 61.4 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 63 - Forks: 4

lvn3668/naivevariantcaller_ECGR_variantdetection

Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5

Language: Python - Size: 2.39 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

suhrig/arriba

Fast and accurate gene fusion detection from RNA-Seq data

Language: C++ - Size: 24.1 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 206 - Forks: 49

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.

Size: 137 KB - Last synced: 16 days ago - Pushed: about 1 month ago - Stars: 11 - Forks: 0

sanger-tol/variantcalling

This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.

Language: Nextflow - Size: 3.45 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

kaist-ina/RUN-DVC

Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning

Language: Python - Size: 3.5 MB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 8 - Forks: 0

tobiasrausch/covid19

SARS-CoV-2 analysis pipeline for short-read, paired-end illumina sequencing

Language: Python - Size: 324 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 6 - Forks: 1

tsnorri/panvc3

Variant calling using a pan-genomic reference, version 3

Language: C++ - Size: 832 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

rice-systems/lofreq-fpga

FPGA Acceleration for the LoFreq variant caller

Language: C - Size: 20.5 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 0

BiodataAnalysisGroup/synth4bench Fork of sfragkoul/synth4bench

A framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.

Language: R - Size: 54.7 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 1 - Forks: 0

nf-core/rnavar

gatk4 RNA variant calling pipeline

Language: Nextflow - Size: 3.62 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 28 - Forks: 29

CMU-SAFARI/Genome-on-Diet

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

Language: Roff - Size: 63 MB - Last synced: 6 days ago - Pushed: 7 months ago - Stars: 11 - Forks: 4

BioJulia/SequenceVariation.jl

Biological sequence variation

Language: Julia - Size: 371 KB - Last synced: 18 days ago - Pushed: about 1 year ago - Stars: 9 - Forks: 3

PacificBiosciences/ccs

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

Size: 34.1 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 105 - Forks: 31

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 143 - Forks: 28

sufyazi/tfbs-variant-calling-nf

Repository detailing a Nextflow pipeline to run mpileup variant callling on TF footprints.

Language: HTML - Size: 21.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

sfragkoul/synth4bench

A framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms for the needs of my Doctoral Thesis.

Language: R - Size: 54.7 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 0 - Forks: 1

bguo068/snp_call_nf

Nextflow pipeline for plasmodium SNP calling

Language: Nextflow - Size: 105 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 2

ShujiaHuang/ilus

A handy variant calling pipeline generator for whole-genome 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.

Language: Python - Size: 780 KB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 102 - Forks: 32

paq88/Variant_Calling_Nextflow_pipeline

Pipeline for SNP Calling Created in Nextflow management system for purposesof testing the advantages of managed systems vs native applications in variant calling. The paper created and published one day is titled "NextFlow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data"

Language: Nextflow - Size: 8.79 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0

czbiohub-sf/cerebra 📦

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

Language: Python - Size: 164 MB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 59 - Forks: 9

sateeshperi/nextflow_varcal

Nextflow Tutorial - Variant Calling Edition

Language: HTML - Size: 70 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 2

sfragkoul/Varscan2VCF Fork of scchess/Varscan2VCF

Convert VarScan output to VCF format

Language: Python - Size: 3.85 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

kevlar-dev/kevlar

Reference-free variant discovery in large eukaryotic genomes

Language: Python - Size: 71.5 MB - Last synced: 15 days ago - Pushed: almost 3 years ago - Stars: 40 - Forks: 9

VCCRI/dv-trio

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

Language: Shell - Size: 165 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 8 - Forks: 1

kevin-wamae/snakemake-illuminaVarGATK

A Snakemake workflow for variant calling using GATK4 best practices

Language: Python - Size: 46.5 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 2

sib-swiss/NGS-variants-training

GitHub for the SIB courses NGS - Genome variant analysis

Language: Shell - Size: 68.1 MB - Last synced: 19 days ago - Pushed: 2 months ago - Stars: 24 - Forks: 9

x-zang/tutorial-gatk4-rnaseq-germline-snps-indels

Beginner's tutorial for GATK4 workflow on variant calling from RNA-seq.

Size: 30.3 KB - Last synced: 3 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 1

PulmonomicsLab/mcdr-mtb-standalone

Multi-class classification of drug resistance in MTB clinical isolates

Language: Shell - Size: 5.56 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

anand-imcm/pb-variant-call

Variant Calling and Annotation using PacBio Hi-Fi Reads

Language: WDL - Size: 59.6 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

luntergroup/octopus

Bayesian haplotype-based mutation calling

Language: C++ - Size: 137 MB - Last synced: 3 months ago - Pushed: 9 months ago - Stars: 291 - Forks: 37

aquaskyline/Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Language: Python - Size: 894 MB - Last synced: about 4 hours ago - Pushed: 4 months ago - Stars: 172 - Forks: 27

arunkumarramesh/Plant-Methylome-Evolution

Pipelines to identify polymorphic genetic and methylation variants

Language: Shell - Size: 115 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

LauraSkak/Modification-count-workflow

This workflow uses Dorado, Samtools, Clair3, WhatHap and Modkit to extract a modification count table containing information for each relevant site.

Language: Python - Size: 225 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

NCI-CGR/HPV_low_VAF_SNV_prediction

Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning

Language: Jupyter Notebook - Size: 17.3 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

areebapatel/Rapid-CNS2 📦

Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

Language: Shell - Size: 572 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

KevinDelGaudio/SNVfromVCF

A simple tool for SNP mutation type determination.

Language: R - Size: 272 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

datasnakes/pyVariant 📦

A pipeline to call variants for RNASeq implemented with python.

Size: 0 Bytes - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

elbecerrasoto/variants

Variant Calling Snakemake Pipeline

Language: Python - Size: 389 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

nf-core/exoseq 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 2.77 MB - Last synced: 4 months ago - Pushed: over 5 years ago - Stars: 14 - Forks: 25

nf-core/deepvariant Fork of lifebit-ai/DeepVariant 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 7.18 MB - Last synced: 4 months ago - Pushed: almost 3 years ago - Stars: 40 - Forks: 18

auroramaurizio/my_DNA_seq_pipelines

In this repository I backup the pipelines I write for the project I am involved

Language: Python - Size: 2.85 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

kevin-wamae/PlasmoSeq-DualTech

A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries

Language: Python - Size: 8.76 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 2

bioinformatics-centre/BayesTyper

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

Language: C++ - Size: 1.75 MB - Last synced: 5 months ago - Pushed: about 5 years ago - Stars: 83 - Forks: 8

bpucker/NAVIP

Neighborhood-Aware Variant Impact Predictor

Language: Python - Size: 179 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 1

EUCANCan/variant-callers

Scripts and containers to run the variant callers originally used in ONCOLINER

Language: Shell - Size: 247 MB - Last synced: about 24 hours ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

CMU-SAFARI/Molecules2Variations

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957

Size: 4.31 MB - Last synced: 6 days ago - Pushed: almost 2 years ago - Stars: 8 - Forks: 0

gear-genomics/verdin

Variant Primer Design

Language: Python - Size: 85 KB - Last synced: 18 days ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0

gear-genomics/indigo

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

Language: JavaScript - Size: 2.72 MB - Last synced: 18 days ago - Pushed: 6 months ago - Stars: 30 - Forks: 6