eichlerlab Goto Github PK

align_all

A general read-alignment pipeline for PacBioHiFi, ONT, and Illumina data.

aou_wdl

Repository for storing WDL workflows for execution in the AoU Researcher Workbench

assembly_compare_ref_query

Assess the QV of an assembly

assembly_eval

assembly_qc

assembly QC pipeline starts with foreign contamination screening

aws

This is the github repository for the Eichler lab Amazon Web Services (AWS) pipelines

back-reference-qc

Detect outlier long-reads by using its Illumina counterpart.

basecall_dorado

Snakemake repository for basecalling with dorado

bax2bam

A pipeline for automating bax2bam (PacBio) over many cells per sample

blasr

This is an unsupported version of the PacBio blasr aligner. It contains my (very beta) optimizations and new functionality. It may disappear at any time.

browser_shots_for_cnv

Creates a pdf booklet of tracks for visualizing array CGH / RPKM per family for large cohorts

browser_tracks

Pipelines to create browser track compatible files from raw files

ccs_stats

Pipeline for generating CCS sequence run summaries

cdr-finder

CDR-Finder

chm1_scripts

clone_mapping

Pipeline for generating SUNK pileups from clone sequence data

compteam_tools

A collection of custom scripts for everyday long read analysis

continuous-methylation

A Snakemake pipeline for methylation analysis using long-read sequencing (third generation).

cost_center_scripts

current a single script for Katy and Melanie

daligner

Find all significant local alignments between reads

data_table

Variant and annotation integration

demultiplex

Demultiplex Illumina runs by barcode

denovo_sv_validation

Pipeline for validation of de novo SVs

docker_hub

Repository for Testing Automatic Builds with Docker Hub

dss-snakemake

A Snakemake pipeline for differential methylation analysis using DSS

fastcn-smk

find_sunks

Pipeline to extract SUNKs from a given assembly

great_ape_assembly_analyses

Code for analyses of great ape assemblies used in Kronenberg et al. 2017/8

hgsvc_ena

Pipeline for pushing data to ENA for HGSVC

hgsvg

Analysis code for 1kg