Release notes

Recently published apps

The following tools were updated to their latest versions and upgraded to CWL1.x:

• HISAT2-StringTie workflow

• StringTie

• Hisat2

• Trimmomatic

• Tabix

• SBG FASTQ Merge

The following new apps were published, in CWL1.x:

• Exomiser 12.1.0 - tool for prioritizing variants from WES and WGS data.

• VEP Slivar Trios Rare Diseases Analysis workflow - analyzes WES and WGS family variants.

• Clustering and Gene Marker Identification with Seurat 3.2.2 - clustering and gene marker identification analysis starting from gene-cell UMI or read counts.

• xCell 1.3 - tool for cell type enrichment analysis, which takes gene expression data and performs analysis for 64 immune and stromal cell types.

• MBASED 1.18.0 tool - used for performing allele specific expression analysis.

• MBASED workflow - based on the MBASED tool, with added phasing and VEP annotation, the workflow allows for easier running of allele specific expression analysis.

• elPrep 4.1.6 - high-performance tool for preparing SAM/BAM files for variant calling in sequencing pipelines, which can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, calculating and applying base quality score recalibration, etc.

• Kraken2 2.0.9 - taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.

• Bracken 2.5 - uses the taxonomic assignments made by Kraken/Kraken2, along with information about the genomes themselves, to estimate abundance at the species/genus level, or above.

• Metagenomics Profiling with Kraken2 - workflow used for metagenomic classification, abundance estimation and visualization.

• cuteSV 1.0.9 - structural variant discovery tool designed for long read sequences.

• Sniffles 1.0.12b - structural variation caller for PacBio or Oxford Nanopore data.

• NanoPlot 1.33.0 - plotting QC tool for long reads sequencing data.

• goleft IndexCov 0.2.4 - used to quickly (in minutes) assess the coverage distribution (16KB resolution) of a WGS cohort from BAI/CRAI files, or infer sex (by plotting the inferred copy number of sex chromosomes).

• vcfanno 0.3.2 - used to annotate variants with information from VCF, BED or BAM sources.

• vcf2db - converts an annotated VCF file into a Gemini-compatible database.

• Cas-OFFinder 2.4 - tool that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.

• BitMapperBS 1.0.2.3 - toolkit for processing WGBS (whole-genome bisufite) reads from directional protocol.

• MethylDackel 0.5.1 - toolkit for processing BS-seq alignments and extracting per-base methylation metrics from them.

• WGBS Analysis BitMapperBS with MethylDackel workflow - developed for BS-seq reads processing and DNA methylation analyses.

• CRISPResso2 2.0.44 - used for analyzing genome editing experiments (public on academic platforms only).

• SAIGE 0.39 - single-variant association tests for binary traits and quantitative traits.

• PRSice-2 2.3.3 - tool for polygenic risk score (PRS) analyses.

• PheWAS R workflow - can be used to conduct PheWAS analyses.

• ONT WGS Data Processing workflow basic workflow for processing Oxford Nanopore WGS data.