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.

Marko Marinkovic