Smoother

Smoother is an interactive analysis and visualization software for contact mapping data.

Quick Start

❗ If you want an in-detail explanation of installing Smoother and doing a handful of first steps, how about taking a tour 🚌?

Otherwise, here is a brief set of instructions to get Smoother running: First, install conda on your machine if you don't have it already.

Then, create & activate a new environment (optional)

 conda create -y -n smoother python=3.9
 conda activate smoother

Install Smoother (and all requirements) using pip. Smoother runs under Windows, Linux, and MacOS using the Google Chrome, Safari, or Firefox browsers.

 pip install biosmoother
 conda install -y nodejs cairo # pip cannot install nodejs and cairo, so we use conda

Download the example Smoother indices. If you are on Ubuntu or MaxOS, run the following commands:

 conda install -y wget unzip
 wget https://syncandshare.lrz.de/dl/fiTWvK4pxwB2TQkMSrzzDJ/t_brucei_hi_c.smoother_index.zip
 #wget https://syncandshare.lrz.de/dl/fi8NBv2b3VDt4Htkm8Auuv/m_musculus_radicl_seq.smoother_index.zip
 
 unzip t_brucei_hi_c.smoother_index.zip
 #unzip m_musculus_radicl_seq.smoother_index.zip

On Windows, run this instead:

 curl.exe https://syncandshare.lrz.de/dl/fiTWvK4pxwB2TQkMSrzzDJ/t_brucei_hi_c.smoother_index.zip --output t_brucei_hi_c.smoother_index.zip
 #curl.exe https://syncandshare.lrz.de/dl/fi8NBv2b3VDt4Htkm8Auuv/m_musculus_radicl_seq.smoother_index.zip --output m_musculus_radicl_seq.smoother_index.zip
 
 tar -xf t_brucei_hi_c.smoother_index.zip
 #tar -xf m_musculus_radicl_seq.smoother_index.zip

View one of the indices (Ubuntu, MacOs & Windows)

 biosmoother serve t_brucei_hi_c.smoother_index --show
 #biosmoother serve m_musculus_radicl_seq.smoother_index --show

From now on, to run smoother you will merely have to activate the environment and run the serve command.

 conda activate smoother
 biosmoother serve t_brucei_hi_c.smoother_index --show

Full Documentation

For more information and in-depth instructions, check out the manual.

Overview

In Smoother, parameters can be changed on-the-fly. This means, a user can click a button or move a slider and will immediately see the effect of that parameter change on screen. Parameters that can be changed include:

Here is a screenshot of Smoother in action:

Loading your own data

All data needs to be converted into a Smoother index first. For this, first create an empty index:

biosmoother init my_index -a my_annotation.gff

Here, my_annotation.gff is a GFF file that contains the genomes annotations.

Then, add your data to the index:

biosmoother repl my_index my_replicate_1.tsv name_of_replicate_1
biosmoother repl my_index my_replicate_2.tsv name_of_replicate_2
...

Here my_replicate_x.tsv needs to be a tab-separated file with 10 columns: read_id, chr1, pos1, chr2, pos2, strand1, strand2, pair_type, mapq1, and mapq2.

Finally, the index can be opened with:

biosmoother serve my_index --show

Cite

If you use smoother in your research, please cite:

Markus R Schmidt, Anna Barcons-Simon, Claudia Rabuffo, T Nicolai Siegel, Smoother: on-the-fly processing of interactome data using prefix sums, Nucleic Acids Research, 2024; gkae008, https://doi.org/10.1093/nar/gkae008