Pinned Repositories
chm1_scripts
indel_correction_pipeline
new falcon assemblies that have been quivered and Pilon polished still have heterozygote indel errors. This pipeline will correct most of them.
pacbio_variant_caller
SMRT-SV: Structural variant and indel caller for PacBio reads
pav
Phased assembly variant caller
smrtsv2
Structural variant caller
sratools
Tools for downloading and processing data from the Sequence Read Archive (SRA)
svpop
Variant annotation and merging pipeline
ultra_rare_transmitted
Pipeline to generate ultra-rare transmitted callsets for genomes and exomes
vcf-flow
Convert tab-delimited file into a VCF
WGAC
Scripts used for whole genome analysis comparison (WGAC)
Eichler Lab's Repositories
EichlerLab/pav
Phased assembly variant caller
EichlerLab/svpop
Variant annotation and merging pipeline
EichlerLab/WGAC
Scripts used for whole genome analysis comparison (WGAC)
EichlerLab/ONT_pipelines
EichlerLab/pbsv
PBSV automated pipeline
EichlerLab/denovo_sv_validation
Pipeline for validation of de novo SVs
EichlerLab/docker_hub
Repository for Testing Automatic Builds with Docker Hub
EichlerLab/hifiasm-smk
Snakemake software repo for hifiasm
EichlerLab/long-reads-public-codebase
This Repo will be for the sharing of code for the long reads analysis initiative.
EichlerLab/ont_stats
Pipeline for getting sequencing statistics from ONT FASTQs
EichlerLab/read_depth_genotyper
Get genotypes for regions using WSSD and SUNK
EichlerLab/seqtools
EichlerLab/AoU_WDL
Repository for storing WDL workflows for execution in the AoU Researcher Workbench
EichlerLab/align_all
A general read-alignment pipeline for PacBioHiFi, ONT, and Illumina data.
EichlerLab/assembly_eval
EichlerLab/assembly_qc
assembly QC pipeline starts with foreign contamination screening
EichlerLab/back-reference-qc
Detect outlier long-reads by using its Illumina counterpart.
EichlerLab/basecall_dorado
Snakemake repository for basecalling with dorado
EichlerLab/ccs_stats
Pipeline for generating CCS sequence run summaries
EichlerLab/CDR-Finder
CDR-Finder
EichlerLab/compteam_tools
A collection of custom scripts for everyday long read analysis
EichlerLab/continuous-methylation
A Snakemake pipeline for methylation analysis using long-read sequencing (third generation).
EichlerLab/data_table
Variant and annotation integration
EichlerLab/dss-snakemake
A Snakemake pipeline for differential methylation analysis using DSS
EichlerLab/fastCN-smk
EichlerLab/reassign-sex-chr
Pipeline for reassigning duplicated or fragmented sex chromosomes to isolated haplotypes
EichlerLab/sedef
Interconnected snakemake workflows for annotation and analysis of assemblies
EichlerLab/subseq
Pipeline for validating variant calls with support from individual reads
EichlerLab/subseq-smk
Snakemake pipeline which leverages subseq to validate structural variants
EichlerLab/sv-path-predictor
A pipeline to predict structural variant pathogenicity with an aggregated score.