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    34 repositories

    • bamkit

      Public
      Tools for common BAM file manipulations
      Python
      •
      MIT License
      •6•2•2•1•Updated Apr 4, 2024Apr 4, 2024

    • competitive-alignment

      Public
      Shell
      •2•10•0•0•Updated Jun 8, 2023Jun 8, 2023

    • cromulent

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated May 22, 2023May 22, 2023

    • speedseq

      Public
      A flexible framework for rapid genome analysis and interpretation
      C
      •
      MIT License
      •117•315•70•5•Updated Oct 18, 2022Oct 18, 2022

    • assembly_validation

      Public
      Python
      •
      MIT License
      •1•5•0•0•Updated Jun 10, 2022Jun 10, 2022

    • svtools

      Public
      Tools for processing and analyzing structural variants.
      bioinformaticsstructural-variation
      Python
      •
      MIT License
      •54•150•66•4•Updated May 2, 2022May 2, 2022

    • cromwell-deployment

      Public
      Scripts and configuration to setup a Cromwell deployment
      Python
      •
      ISC License
      •3•2•4•0•Updated Dec 14, 2021Dec 14, 2021

    • sv-pipeline

      Public
      Pipeline for structural variation detection in cohorts
      bioinformaticsgenomicsstructural-variation
      WDL
      •20•49•11•0•Updated Sep 14, 2021Sep 14, 2021

    • lah

      Public
      Local Assembly of Haplotypes
      Python
      •
      MIT License
      •1•0•0•1•Updated Mar 25, 2021Mar 25, 2021

    • cloud-polices

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Mar 25, 2021Mar 25, 2021

    • svtyper

      Public
      Bayesian genotyper for structural variants
      bioinformaticsgenomicsvcfgenotype
      Python
      •
      MIT License
      •55•127•45•4•Updated Mar 6, 2021Mar 6, 2021

    • tenx-gcp

      Public
      Run 10X Genomics Software in Google Cloud Deployments
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 22, 2021Feb 22, 2021

    • FinnSV_paper_1220

      Public
      The summary statistics of FinMetSeq SV paper
      0•0•0•0•Updated Dec 3, 2020Dec 3, 2020

    • gatk4-germline-snv-pipeline

      Public
      GATK4 pipeline for joint variant calling (SNP/INDELs)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jul 7, 2020Jul 7, 2020

    • CADD-scripts

      Public
      CADD scripts release for offline scoring. For more information about CADD, please visit our website
      Python
      •
      Other
      •34•0•0•0•Updated Jun 9, 2020Jun 9, 2020

    • sv_paper_042020

      Public
      supplementary data for abel et al paper
      1•4•0•0•Updated Apr 8, 2020Apr 8, 2020

    • old-laims

      Public
      Python
      •4•0•2•0•Updated Jan 24, 2020Jan 24, 2020

    • cluster_intro

      Public
      Hall Lab Computing 101
      0•2•0•0•Updated Nov 20, 2019Nov 20, 2019

    • ArrowGrid

      Public
      Shell
      •
      Other
      •4•0•0•0•Updated Aug 13, 2019Aug 13, 2019

    • crimson

      Public
      Bioinformatics tool outputs converter to JSON or YAML
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•0•0•0•Updated Jun 5, 2019Jun 5, 2019

    • fastqtl

      Public
      Fork of FastQTL for SVs
      C++
      •
      GNU General Public License v3.0
      •12•5•4•0•Updated Dec 17, 2018Dec 17, 2018

    • extract_sv_reads

      Public archive
      Tool for extracting splitter or discordant reads from a BAM or CRAM file.
      Python
      •
      MIT License
      •0•4•2•0•Updated Oct 12, 2018Oct 12, 2018

    • 1kg_sv_comparison

      Public
      Python
      •
      MIT License
      •1•4•0•0•Updated Sep 7, 2017Sep 7, 2017

    • long-read-validation

      Public
      Long-read validation of BEDPE structural variation
      Python
      •3•9•1•0•Updated Sep 7, 2017Sep 7, 2017

    • soup

      Public
      Catch-all for uncategorized or project-specific scripts 🍵
      C
      •2•0•0•0•Updated Jun 7, 2017Jun 7, 2017

    • lumpy-sv

      Public
      lumpy: a general probabilistic framework for structural variant discovery
      C
      •
      MIT License
      •119•0•0•0•Updated Apr 17, 2017Apr 17, 2017

    • pipelines-api-examples

      Public
      Examples for the Google Genomics Pipelines API.
      Python
      •
      Apache License 2.0
      •27•0•0•0•Updated Apr 11, 2017Apr 11, 2017

    • gtex

      Public
      GTEx analysis scripts
      Python
      •8•20•1•0•Updated Mar 14, 2017Mar 14, 2017

    • cshl_sv_2016

      Public
      Python
      •0•2•0•0•Updated Nov 10, 2016Nov 10, 2016

    • io

      Public
      i/o tools
      Python
      •0•2•0•0•Updated Sep 8, 2016Sep 8, 2016