Dan Lu's repositories
nextflow_cheatsheet
Tips for Nextflow and cheatsheet for channel operation
Fuller_Lab_paper
Scripts/tutorial to reproduce data analysis for the genomics paper from the Fuller Lab
NGS_workshop
Made this for very beginners of next-generation sequencing and high performance computing cluster
bactopia.github.io
Bactopia Documentation
bug_report_data
temp toy data for bug report
cegwas2-nf
GWA mapping with C. elegans
CENTIPEDE.tutorial
:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
czid-workflows
Portable WDL workflows for CZ ID production pipelines
genome_prep
download and index genome for alignment and variant calling
monkeypox
Nextstrain build for monkeypox virus
ncov
Nextstrain build for novel coronavirus SARS-CoV-2
ncov-ingest
A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
Nextflow_training
Code for Nextflow trau
nf_qc
Quick QC and trim for raw sequencing reads
pp-sketchlib
Library of sketching functions used by PopPUNK
wi-gatk
The new GATK-based pipeline for wild isolate C. elegans strains