{"title":"Release note 02.08.21","slug":"release-note-020821","body":"## Recently published apps\n\nThe following tools were updated to their latest versions and upgraded to CWL1.x:\n\n  * HISAT2-StringTie workflow\n  * StringTie\n  * Hisat2\n  * Trimmomatic\n  * Tabix\n  * SBG FASTQ Merge\n\nThe following new apps were published, in CWL1.x:\n\n* **Exomiser 12.1.0** - tool for prioritizing variants from WES and WGS data.\n* **VEP Slivar Trios Rare Diseases Analysis workflow** - analyzes WES and WGS family variants.\n* **Clustering and Gene Marker Identification with Seurat 3.2.2** - clustering and gene marker identification analysis starting from gene-cell UMI or read counts.\n* **xCell 1.3** - tool for cell type enrichment analysis, which takes gene expression data and performs analysis for 64 immune and stromal cell types.\n* **MBASED 1.18.0 tool** - used for performing allele specific expression analysis.\n* **MBASED workflow** - based on the MBASED tool, with added phasing and VEP annotation, the workflow allows for easier running of allele specific expression analysis.\n* **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.\n* **Kraken2 2.0.9** - taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.\n* **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.\n* **Metagenomics Profiling with Kraken2** - workflow used for metagenomic classification, abundance estimation and visualization.\n* **cuteSV 1.0.9** - structural variant discovery tool designed for long read sequences.\n* **Sniffles 1.0.12b** - structural variation caller for PacBio or Oxford Nanopore data.\n* **NanoPlot 1.33.0** - plotting QC tool for long reads sequencing data.\n* **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).\n* **vcfanno 0.3.2** - used to annotate variants with information from VCF, BED or BAM sources.\n* **vcf2db** - converts an annotated VCF file into a Gemini-compatible database.\n* **Cas-OFFinder 2.4** - tool that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.\n* **BitMapperBS 1.0.2.3** - toolkit for processing WGBS (whole-genome bisufite) reads from directional protocol.\n* **MethylDackel 0.5.1** - toolkit for processing BS-seq alignments and extracting per-base methylation metrics from them.\n* **WGBS Analysis BitMapperBS with MethylDackel workflow** - developed for BS-seq reads processing and DNA methylation analyses.\n* **CRISPResso2 2.0.44** - used for analyzing genome editing experiments (public on academic platforms only).\n* **SAIGE 0.39** - single-variant association tests for binary traits and quantitative traits.\n* **PRSice-2 2.3.3** - tool for polygenic risk score (PRS) analyses.\n* **PheWAS R workflow** - can be used to conduct PheWAS analyses.\n* **ONT WGS Data Processing workflow** - basic workflow for processing Oxford Nanopore WGS data.","_id":"602154d1919a0d0011a8196b","changelog":[],"createdAt":"2021-02-08T15:12:17.005Z","user":{"name":"Marko Marinkovic","username":"","_id":"5767bc73bb15f40e00a28777"},"initVersion":{"version":"1.0","_id":"5773dcfc255e820e00e1cd50"},"project":"5773dcfc255e820e00e1cd4d","__v":0}

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 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.