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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 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.