Release notes - May 10, 2024
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 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+.
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.