---
agentTools:
  projectIndex: https://docs.cavatica.org/llms.txt
---

# Release note 05.10.24

## Recently published apps

### snM3C pipeline

The snM3C pipeline is designed for profiling 3D genome structure and DNA methylation in single cell data as a part of the Human Cell Atlas and the WARP BRAIN Initiative.

The snM3C pipeline performs:

* Demultiplexing (by the Demultiplexing custom tool)
* Reads sorting (by the Sort custom tool)
* Reads trimming (by Cutadapt)
* Paired-end reads alignment (by Hisat-3n)
* Separating unmapped, uniquely aligned, and multi-aligned reads (by Separate unmapped reads wrapped around a custom script)
* Splitting unmapped reads by enzyme cut site (by Split unmapped reads wrapped around a custom script)
* Alignment of the unmapped, single-end reads (by Hisat-3n)
* Removing the overlapping reads (by Remove overlap read parts wrapped around a custom script)
* Merging mapped reads from single- and paired-end alignments (by Samtools Merge)
* Removing duplicate reads (by Picard MarkDuplicates)
* Calling chromatin contacts (by Call chromatin contacts wrapped around the custom script)
* Creating ALLC files (by Allcools bam-to-allc)
* Creating summary output (by Allcools extract-allc)

All tools are wrapped for the workflow specifically and use retagged [us.gcr.io/broad-gotc-prod/m3c-yap-hisat:1.0.0-2.2.1](https://console.cloud.google.com/gcr/images/broad-gotc-prod/US/m3c-yap-hisat:1.0.0-2.2.1/details?pli=1) Docker image.

### DeepSomatic 1.6.1

**DeepSomatic** is an extension of DeepVariant for calling somatic variants from matched tumor-normal data. The tool is still in active development and only WGS data is currently supported.

### SortMeRNA 4.3.6

**SortMeRNA** is a local sequence alignment tool for filtering, mapping and OTU clustering. The main applications of SortMeRNA are filtering rRNA from metatranscriptomic data, OTU-picking and taxonomy assignation available through [QIIME v1.9+](http://qiime.org/).

### dupRadar 1.32.0

The **dupRadar** tool is intended for duplication rate quality control for RNA-Seq data. It gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it.