High Performance Computing in Biology
High performance computational biology at the University of Illinois
University of Illinois at Urbana-Champaign
Pinned Repositories
16S-rDNA-dada2-pipeline
**DEFUNCT** dada2-based Nextflow pipeline for multiple amplicon data. See website for up-to-date version
caceres-16S-mosquito-2022Sept
Data-Management
Data Carpentry data management course, combining CSE and HPCBio materials
eib-marker-design
Workflow for designing KASP markers from resequencing data
EMIRGE
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
hergenrother-16S-mouse-2022Sept
Code for the Hergenrother 2022 mouse antimicrobiall study
In-depth-NGS-Data-Analysis-Course
Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.
Intro-to-ChIPseq
Intro to ChIPseq using HPC
LifeSciTrainingSlack
A Slack community of people who do short-format training in the life sciences
R-genomics
Lesson on data analysis and visualization in R for genomics
High Performance Computing in Biology's Repositories
HPCBio/eib-marker-design
Workflow for designing KASP markers from resequencing data
HPCBio/caceres-16S-mosquito-2022Sept
HPCBio/hergenrother-16S-mouse-2022Sept
Code for the Hergenrother 2022 mouse antimicrobiall study
HPCBio/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
HPCBio/bacterial_variant_calling
A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker
HPCBio/configs
Config files used to define parameters specific to compute environments at different Institutions
HPCBio/CPG
Building a Chinese pan-genome of 486 individuals
HPCBio/cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
HPCBio/Detect-seq
An unbiased method for genome-wide CBE off-targets assessment
HPCBio/EM-seq
Tools and Data related to Enzymatic Methylation Sequencing
HPCBio/figaro
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
HPCBio/GFF3toolkit
Python programs for processing GFF3 files
HPCBio/Li_scATACSeq_demultiplexing_Nov23
HPCBio/Mayo-Genome-Assembly
HPCBio/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
HPCBio/methylseq-old
Old copy of the nf-core methylseq workflow including hacked in NuGen/Tecan support
HPCBio/microbial-profiling
HPCBio's Microbial Profiling Analysis workshop page
HPCBio/NBISweden-pipelines-nextflow
NBIS nextflow pipelines framework
HPCBio/nextflow-training
Nextflow training material
HPCBio/NuMetRRBS
HPCBio/Pangenome-Graphs-Workshop
This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.
HPCBio/phyloseq-extended
Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul
HPCBio/plotly_microbiome
R helper functions for making Plotly graphs in microbiome work
HPCBio/reference_database_creator
creating reference databases for amplicon sequencing
HPCBio/Refgraph_pipeline
H3ABioNet RefGraph assembly-based pipeline
HPCBio/smrnaseq
A small-RNA sequencing analysis pipeline
HPCBio/spams-R
R interface for SPAMS (SPArse Modeling Software)
HPCBio/TRIDENT
NGS variant analysis & fluctuation analysis MLE calculator
HPCBio/varcall
Nextflow scripts for doing variant calling on human samples
HPCBio/workflows-nextflow
Workflow management with Nextflow and nf-core