Release note

Written by Marko Marinkovic in

on May 10th, 2024

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 Docker image.

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 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+.

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.