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@EichlerLab

Eichler Lab

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  1. pav pav Public

    Phased assembly variant caller

    Python 132 9

  2. smrtsv2 smrtsv2 Public

    Structural variant caller

    Python 55 6

  3. svpop svpop Public

    Variant annotation and merging pipeline

    Python 41 8

  4. pacbio_variant_caller pacbio_variant_caller Public archive

    SMRT-SV: Structural variant and indel caller for PacBio reads

    Python 28 15

  5. CDR-Finder CDR-Finder Public

    Workflow to identify the centromere dip regions (CDR) from methyl BAMs

    Python 11 3

  6. vcf-flow vcf-flow Public

    Forked from huddlej/tab-to-vcf

    Convert tab-delimited file into a VCF

    Python 8 2

Repositories

Showing 10 of 83 repositories
  • assembly_qc Public Forked from youngjun0827/assembly_qc

    assembly QC pipeline starts with foreign contamination screening

    EichlerLab/assembly_qc’s past year of commit activity
    Python 0 1 0 0 Updated Jan 21, 2026
  • sample_qc Public

    Snakemake pipeline for running ntsm to check sample contaminations

    EichlerLab/sample_qc’s past year of commit activity
    Python 0 0 0 0 Updated Jan 20, 2026
  • docker_hub Public

    Repository for Automated Docker Builds with Docker Hub

    EichlerLab/docker_hub’s past year of commit activity
    Python 1 0 0 0 Updated Jan 14, 2026
  • sedef_smk Public

    A snakemake pipeline for SEDEF.

    EichlerLab/sedef_smk’s past year of commit activity
    0 MIT 0 0 0 Updated Jan 5, 2026
  • subseq-smk Public

    Snakemake pipeline which leverages subseq to validate structural variants

    EichlerLab/subseq-smk’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 5, 2026
  • asap Public

    Autism Susceptibility Analysis Pipeline with focus in Structural Variants

    EichlerLab/asap’s past year of commit activity
    Python 1 MIT 1 0 0 Updated Jan 5, 2026
  • hifiasm-smk Public

    Snakemake software repo for hifiasm

    EichlerLab/hifiasm-smk’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Dec 23, 2025
  • reads_processing Public

    Support for quality trimming and downsampling from the longest reads for reads used in assembly construction.

    EichlerLab/reads_processing’s past year of commit activity
    Python 0 0 0 0 Updated Dec 15, 2025
  • assembly_eval Public
    EichlerLab/assembly_eval’s past year of commit activity
    Python 3 0 0 0 Updated Nov 3, 2025
  • compteam_tools Public

    A collection of custom scripts for everyday long read analysis

    EichlerLab/compteam_tools’s past year of commit activity
    Python 0 0 0 0 Updated Oct 17, 2025
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