diff --git a/README.md b/README.md index 192fa0de6b9cfd727673b531668abdfdb38c3e2d..7d94cbaf6a1d1758247fbcf0ee09225d08214f60 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ -# nf-core/hic +#  + **Analysis of Chromosome Conformation Capture data (Hi-C)** [](https://travis-ci.org/nf-core/hic) @@ -10,8 +11,20 @@ https://img.shields.io/badge/singularity-available-7E4C74.svg) ### Introduction +This pipeline is based on the [HiC-Pro workflow](https://github.com/nservant/HiC-Pro). +It was designed to process Hi-C data from raw fastq files (paired-end Illumina data) to normalized contact maps. The current version supports digestion protocols. +Support for other protocols is ongoing. + The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible. +### Pipeline summary +1. Mapping using a two steps strategy to rescue reads spanning the ligation sites (bowtie2) +2. Detection of valid interaction products +3. Duplicates removal +4. Create genome-wide contact maps at various resolution +5. Contact maps normalization using the ICE algorithm (iced) +6. Quality controls and report (MultiQC) +7. Addition export for visualisation and downstream analysis (cooler) ### Documentation The nf-core/hic pipeline comes with documentation about the pipeline, found in the `docs/` directory: @@ -25,7 +38,5 @@ The nf-core/hic pipeline comes with documentation about the pipeline, found in t 4. [Output and how to interpret the results](docs/output.md) 5. [Troubleshooting](docs/troubleshooting.md) -<!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works --> - ### Credits nf-core/hic was originally written by Nicolas Servant.