egenomics

egenomics's Stars

• microsoft/lida

  Automatic Generation of Visualizations and Infographics using Large Language Models

  Language:Jupyter Notebook2.6k3892269

• bactopia/bactopia

  A flexible pipeline for complete analysis of bacterial genomes

  Language:Nextflow3861448767

• brentp/somalier

  fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

  Language:Nim255912635

• FRED-2/OptiType

  Precision HLA typing from next-generation sequencing data

  Language:Python1791511472

• broadinstitute/seqr

  web-based analysis tool for rare disease genomics

  Language:Python173161.7k89

• pha4ge/hAMRonization

  Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

  Language:Python132185325

• nf-core/viralrecon

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

  Language:Nextflow112100160107

• Mykrobe-tools/mykrobe

  Antibiotic resistance prediction in minutes

  Language:Python1031110526

• smithlabcode/falco

  A C++ drop-in replacement of FastQC to assess the quality of sequence read data

  Language:HTML9285110

• MDU-PHL/abritamr

  A pipeline for running AMRfinderPlus and collating results into functional classes

  Language:Python65133012

• vplagnol/ExomeDepth

  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

  Language:C5965726

• nf-core/hlatyping

  Precision HLA typing from next-generation sequencing data

  Language:Nextflow521535130

• iqbal-lab-org/clockwork

  CRyPTIC data processing pipelines

  Language:HTML3286822

• hw538/cfDNAPro

  cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis

  Language:R22642

• Gabaldonlab/jloh

  A tool to extract LOH blocks from VCF, BAM and FASTA data

  Language:Python203112

• pha4ge/hAMRonization_workflow

  Harmonization of AMR predictor tool outputs

  Language:Python2010138

• ssadedin/ximmer

  Ximmer is a system for CNV calling on exome and targeted genomic sequencing

  Language:JavaScript1973810

• nf-core/phaseimpute

  Language:Nextflow161645412

• vicruiser/3Dmapper

  Map genetic variants and protein positions to protein interfaces in 3D

  Language:Python13013

• nch-igm/snvstory

  Rapid and accurate ancestry inference using SNVs.

  Language:Python124127

• GavinHaLab/ichorCNA

  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

  Language:R1121310

• mbhall88/tbpore

  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

  Language:Python116432

• nf-core/pathogensurveillance

  Surveillance of pathogens using population genomics and sequencing

  Language:HTML105

• INSaFLU/docker

  Easy installation for INSaFLU made by docker

  Language:Perl76266

• ForomePlatform/anfisa

  Variant Analysis and Curation Tool (Back-end, REST API and Internal Client)

  Language:Python63313

• GavinHaLab/ichorCNA_offtarget

  Estimating tumor fraction by exploiting the off-target reads from targeted DNA sequencing.

  Language:R64

• MicroBinfie/ESCMID-MGE-2022

  Language:Jupyter Notebook6204

• nf-core/phyloplace

  nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

  Language:Groovy515843

• mouliere-lab/ITSFASTR

  A bioinformatic pipeline for ultra-fast analysis of cfDNA using Oxford Nanopore Technologies sequencing.

  Language:Python4022

• LMG9509/TFM

  Evaluación del impacto del proceso de rarefacción en la detección de comunidades microbianas en datos de amplicones ARNr 16S

  Language:R1100