Release note 02.08.21

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 - 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.