High Performance Computing in Biology's repositories
hergenrother-16S-mouse-2022Sept
Code for the Hergenrother 2022 mouse antimicrobiall study
Refgraph_pipeline
H3ABioNet RefGraph assembly-based pipeline
configs
Config files used to define parameters specific to compute environments at different Institutions
workflows-nextflow
Workflow management with Nextflow and nf-core
spams-R
R interface for SPAMS (SPArse Modeling Software)
reference_database_creator
creating reference databases for amplicon sequencing
nextflow-training
Nextflow training material
smrnaseq
A small-RNA sequencing analysis pipeline
Detect-seq
An unbiased method for genome-wide CBE off-targets assessment
EM-seq
Tools and Data related to Enzymatic Methylation Sequencing
TRIDENT
NGS variant analysis & fluctuation analysis MLE calculator
eib-marker-design
Workflow for designing KASP markers from resequencing data
methylseq-old
Old copy of the nf-core methylseq workflow including hacked in NuGen/Tecan support
methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
plotly_microbiome
R helper functions for making Plotly graphs in microbiome work
GFF3toolkit
Python programs for processing GFF3 files
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
figaro
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
bacterial_variant_calling
A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker
microbial-profiling
HPCBio's Microbial Profiling Analysis workshop page
CPG
Building a Chinese pan-genome of 486 individuals
varcall
Nextflow scripts for doing variant calling on human samples
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
NBISweden-pipelines-nextflow
NBIS nextflow pipelines framework
variant-analysis-workshop
Workshop materials for variant analysis using Bioconductor