Release notes

April 26th, 2021

Recently published apps

The following apps were published in CWL1.x:

  • SRA Toolkit 2.10.8 – NCBI’s collection of tools and libraries for accessing data in Sequence Read Archives format (SRA).
  • SRA Download and Set Metadata a workflow that allows for downloading full SRA datasets and populating any metadata information that goes with the dataset
  • AnnotSV 3.0.7 – structural variant annotation and raking tool.
  • IsoformSwitchAnalyzeR 1.12.0 – a tool for differential splicing analysis, it performs statistical identification of the isoform switching while comparing two sample groups.
  • DRIMSeq 1.16.1 – performs differential transcript usage (DTU) analyses using Dirichlet-multinomial generalized linear models.
  • DEXSeq 1.36.0 – toolkit for testing differential exon usage in comparative RNA-Seq experiments.
  • Differential Exon Usage with DEXSeq 1.36.0 – a workflow constructed out of DEXSeq tools, meant for a comprehensive differential splicing analysis.
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April 19th, 2021

Recently published apps

The following apps were published in CWL1.x:

  • Single Cell Multi Sample Pairwise Differential Expression Workflow – pipeline that performs differential expression analysis on single cell data between pairs of user defined conditions.
  • Minimap2 v2.17 – a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database, tailored for use with long read sequencing technologies.
  • fastqValidator 0.1.1 – checks format correctness of paired-end and single-end FASTQ files.
  • FastP 0.20.1 – ultra-fast FASTQ preprocessor with useful quality control and data-filtering features, including adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of FASTQ data.
  • SBG convert SRA/BAM to FASTQ – an all-in-one tool that converts SRA/SAM/BAM/CRAM files into FASTQ format.
  • SBG Create Expression Matrix – creates aggregated matrices from various types of inputs, most typically from abundance estimates produced by tools like RSEM, Salmon, or Kallisto.
  • SHAPEIT 4.2.1 – phasing tool for sequencing and SNP array data.
  • Regenie 2.0.1 – tool for whole genome regression analysis.
  • UMI-tools 1.1.1 – tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
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April 12th, 2021

Recently published apps

MaxQuant is a tool for quantitative proteomics, designed for analysing large mass-spectrometric data. It takes files with high-resolution, quantitative MS data and produces information about quantification of proteins and PTMs. It can be used for analysing data derived from any major relative quantification techniques (Label-free quantification (LFQ), MS1-level labelling and isobaric MS2-level labelling). Furthermore, it provides quantification algorithms for all common forms of tandem mass (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ) labelling (including higher-plex TMT and multinotch MS3 quantification).

GENESIS Association Results Plotting creates Manhattan and QQ plots from GENESIS association test results with additional filtering and stratification options available. This app with it’s default options is the part of a GENESIS Association testing workflows, however after the association testing is completed users can fine-tune the Manhattan and QQ plots by running this app separately.

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April 5th, 2021

Recently published apps

The following apps were upgraded to CWL1 and had their versions updated as well:

  • GATK
  • Picard
  • VEP toolkit and workflow
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March 22nd, 2021

GDC Datasets version update

As of March 17, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 28.0.

 

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March 8th, 2021

Recently published apps

  • GATK Somatic SNVs and INDELs (Mutect2) 4.1.9.0 can be used to detect SNVs and INDELs in one or more tumor samples from a single individual, with or without a matched normal sample. Assembly implies whole haplotypes and read pairs, rather than single bases, as the atomic units of biological variation and sequencing evidence, improving variant calling.
  • GATK Somatic Create Mutect2 Panel of Normals 4.1.9.0 workflow creates a panel of normals (germline and artifactual sites) for use in other GATK workflows. It takes multiple normal sample callsets produced by GATK Somatic SNVs and INDELs 4.1.9.0 (Mutect2 workflow) tumor-only mode (although it is called tumor-only, normal samples are given as the input) and collates sites present in two or more samples into a sites-only VCF.

Both workflows are composed in reference to the official GATK’s WDLs.

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March 1st, 2021

ImprovementsImproved project organization with project tags 

In order to improve the organization and findability of projects, project tags have been introduced to the Seven Bridges Platform.

Project Admins can now assign tags to projects via the API or through the visual interface. Such tags can be used for filtering purposes when browsing all projects, for projects categorization, and for general custom organization of projects.

The maximum number of tags for a single project is 15, while the maximum number of characters in a single tag is 36. Learn more.

GDC Datasets version update

As of February 22, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 27.0.

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February 8th, 2021

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.
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February 1st, 2021

Recently published apps

  • GATK Broad Best Practice Variant Calling From uBAM – This workflow presents two different BROAD Best Practice workflows incorporated into one – BAM processing and variant calling.
  • Functional Equivalence WGS – This workflow processes WGS data according to the functional equivalence standard.
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