Release notes

Recently published apps

We have published the CNVkit 0.9.9 toolkit for inferring and visualizing copy number from high-throughput DNA sequencing data. The toolkit includes the following tools:

• CNVkit breaks lists the targeted genes in which a segmentation breakpoint occurs.
• CNVkit access calculates the sequence-accessible coordinates in chromosomes from the given reference genome.
• CNVkit diagram draws copy number or segments on chromosomes as an ideogram.
• CNVkit export bed converts segments to a BED file.
• CNVkit export vcf converts segments to a VCF file.
• CNVkit segmetrics calculates summary statistics of individual segments.
• CNVkit scatter plots bin-level log2 coverages and segmentation calls together.
• CNVkit metrics calculates the spread of bin-level copy ratios from the corresponding final segments.
• CNVkit heatmap draws copy number for multiple samples as a heatmap.
• CNVkit genemetrics identifies targeted genes with copy number gain or loss above or below a threshold.
• CNVkit call calls absolute integer copy number for each segment in segmented log2 ratio estimates.
• CNVkit batch is a copy number calling pipeline wrapped into a single tool.

Recently published apps

We have published the following apps:

• SBG Pair FASTQs by Metadata CWL1.2 tool, which accepts a list of FASTQ files and groups them into sub-lists based on the metadata. The sbg:draft-2 version of this tool will also remain available in the Public Apps gallery.
• Upgraded version of the MultiQC (v1.13, CWL1.2) tool, which aggregates results from bioinformatics analyses across many samples into a single report. This wrapper version of MultiQC can also accept inputs from files that were produced by the Salmon Workflow (salmon_quant_archive.tar).

NewSeven Bridges CLI now available for macOS ARM users

In order to make sure all of our users have uniform experience and can make the most out of the Seven Bridges Platform, the Seven Bridges Command Line Interface (SB CLI) is now also available for macOS ARM (M1/M2) users. The new build allows the growing population of users using Apple computers with M1 and M2 chips to install the SB CLI and interact with the Platform from the command line. The macOS ARM version of the SB CLI is available for download from the Platform’s Data Tools section and from the related documentation page.

Disabled accounts can now be reactivated in a snap

Accounts that are locked or disabled due to inactivity can now be automatically reactivated by their owners. A new, streamlined flow allows you to initialize the process by sending a reactivation email to your email address after logging in with your last used credentials. By clicking the link in the email and setting a new password on the platform, you will have unrestricted access to your account and data again.

Recently published apps

We have just published and updated our public apps gallery with:

• GATK VariantEval BETA 4.2.5.0, a tool which is used for evaluating variant calls.
• GATK FilterMutectCalls 4.2.5.0, a tool which is used to filter somatic SNVs and indels called by Mutect2.
• Picard CreateSequenceDictionary 2.25.7, a tool for creating a DICT index file for a sequence.
• WARP ExomeGermlineSingleSample 2.4.4, a pipeline for data pre-processing and variant calling in human WES data.

Recently published apps

We have just published and updated our Public Apps gallery with the BCFtools 1.15.1 toolkit – CWL1.2, containing the following tools:

• BCFtools Annotate – edits VCF files, adds or removes annotations.
• BCFtools Call – calls SNPs/indels (former “view”).
• BCFtools Cnv – calls Copy Number Variations.
• BCFtools Concat – concatenates VCF/BCF files from the same set of samples.
• BCFtools Consensus – creates consensus sequence by applying VCF variants.
• BCFtools Convert – converts VCF/BCF to other formats and back.
• BCFtools Csq – is a haplotype-aware consequence caller.
• BCFtools Filter – filters VCF/BCF files using fixed thresholds.
• BCFtools GTcheck – checks sample concordance, detects sample swaps and contamination.
• BCFtools Index – is used for indexing of VCF/BCF files.
• BCFtools Isec – creates intersections of VCF/BCF files.
• BCFtools Merge – merges VCF/BCF files from non-overlapping sample sets.
• BCFtools Mpileup – generates VCF or BCF containing genotype likelihoods for one or BCFtools multiple alignment files.
• BCFtools Norm – normalizes indels.
• BCFtools Query – transforms VCF/BCF into user-defined formats.
• BCFtools Reheader – modifies VCF/BCF header, changes sample names.
• BCFtools Roh – identifies runs of homo/auto-zygosity.
• BCFtools Sort – sorts VCF/BCF files.
• BCFtools Stats – produces VCF/BCF stats (former “vcfcheck”).
• BCFtools View – subsets, filters and converts VCF and BCF files.

We have also updated our Public Apps gallery with the following tools:

• VCFtools Vcf-sort 0.1.16, which sorts VCF files.
• Picard FixMateInformation 2.25.7, which verifies and fixes mate-pair information in a BAM file.

Recently published apps

We have just published and updated our Public Apps gallery with Regenie 3.1.3, a tool which is used for whole genome regression analysis.

Recently published apps

We have published the following apps in our Public Apps gallery:

• Mosdepth 0.3.3 toolkit: Mosdepth, a tool used for fast depth calculation on WGS, WES or targeted BAM and CRAM files and Mosdepth plot_dist which plots Mosdepth results.
• Personal Cancer Genome Reporter 1.0.3 which is used for functional annotation and classification of somatic variants.
• Cancer Predisposition Sequencing Reporter 1.0.0 which analyzes cancer-predisposing germline variants.

We have also updated versions and published tools from the following two toolkits: SRA (v3.0.0, CWL1.2) and Salmon (v1.5.2, CWL1.2). Tools that got the update are:

• SRA sam-dump that converts SRA data into SAM format. With aligned data, NCBI uses Compression by Reference, which only stores the differences in base pairs between sequence data and the segment it aligns to. The process to restore original data, for example as FASTQ, requires fast access to the reference sequences that the original data was aligned to.
• SRA fasterq-dump that converts SRA data into FASTQ format while using temporary files and multi-threading to speed up the extraction.
• SRA fastq-dump that converts SRA data into FASTQ format.
• Salmon Alevin that introduces a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data.
• Salmon Index that builds an index necessary for the Salmon Quant and Salmon Alevin tools. To create an index, it uses a transcriptome reference file in FASTA format. Additionally, one can provide a genome reference along with the transcriptome to create a hybrid index compatible with the improved mapping algorithm named Selective Alignment.

Recently published apps

We have published three VarDict (v1.8.3, CWL1.2) tools and one workflow:

• VarDictJava is the VarDict variant caller Java port. It can be used to call SNPs, MNVs, small indels or complex variants from DNA or RNA alignments. VarDictJava can be used for amplicon-based variant calling and supports both single sample and paired sample analysis.
• VarDict var2vcf_valid, a CWL tool that takes VarDict variants tabular file and outputs variants in VCF format.
• VarDict var2vcf_paired, a CWL tool that converts VarDict tabular output to VCF.
• VarDict Variant Calling workflow (also VarDict v1.8.3, CWL1.2), which can be used for single sample and paired sample variant calling using VarDictJava starting from WES, WGS or amplicon data.

We have also published the following workflows and a toolkit:

• CNVnator Analysis workflow 0.4.1 for CNV calling by doing read-depth (RD) analysis of input BAM files.
• CNVpytor workflow 1.1 for CNV/CNA detection and analysis based on read depth and allele imbalance in WGS.
• PureCN workflow 1.22.0 for estimating tumor purity and ploidy, copy number and loss of heterozygosity (LOH) and PureCN NormalDB workflow which builds a normal database used for coverage normalization in PureCN workflow 1.22.0.
• FACETS workflow 0.6.1 for allele-specific copy number analysis (ASCN).
• Tabix BGZIP 1.14.0 for compressing/decompressing (BAM, VCF, BED, …) any file in BGZF and from BGZF format and Tabix Index 1.14.0 which indexes a TAB-delimited genome position file IN.TAB.BGZ.

NewData Cruncher and Interactive Analysis become Data Studio and Interactive Browsers

Data Studio, previously Data Cruncher, is an interactive analysis tool which allows you to explore and visualize data using environments like JupyterLab and RStudio. Previously located under the Interactive Analysis tab, it has now been given a more prominent location in the project navigation by having its own tab located next to Tasks. With the removal of Data Studio from the Interactive Analysis tab, the tab’s name has been changed to Interactive Browsers in order to better reflect its contents.

Recently published apps

We have just published an updated version (4.2.5.0) of Mutect2 workflows:

• GATK Somatic SNVs and INDELs (Mutect2) 4.2.5.0, a workflow used for somatic short variant calling. It runs on a single tumor-normal pair or on a single tumor sample, and performs additional filtering and functional annotation tasks, and
• GATK Create Mutect2 Panel of Normals 4.2.5.0 that creates a panel of normals for use in other GATK workflows. The workflow takes multiple normal sample callsets and passes them to GATK Somatic SNVs and INDELs (Mutect2) 4.2.5.0 with tumor-only mode (although it is called tumor-only, normal samples are given as the input) and additionally collates sites present in two or more samples into a sites-only VCF.
• Three apps from the MetaXcan toolkit:
  • S-PrediXcan for computing associations between omic features and a complex trait starting from GWAS summary statistics.
  • S-MultiXcan for computing association from predicted gene expression to a trait, using multiple studies for each gene.
  • MetaMany for serially performing multiple MetaXcan runs on a GWAS study from summary statistics using multiple tissues.
• The MetaXcan Workflow for computing associations between omic features and complex traits across multiple tissues. The workflow includes two tools from MetaXcan framework – MetaMany and S-MultiXcan and it uses summary statistics from a GWAS study and multiple models that predict the expression or splicing quantification.
• MaxQuant (v2.0.3.0, CWL1.2), a quantitative proteomics tool designed for analysing large mass-spectrometric data. It uses a target-decoy search strategy to estimate and control the extent of false positives. Within the target-decoy strategy, MaxQuant applies the concept of posterior error probability (PEP) to integrate multiple peptide properties (e.g. length, charge, number of modifications) together with Andromeda score into a single quantity, reflecting the quality of a peptide spectrum match (PSM).
• Manta (v1.6.0, CWL1.2), a tool used for calling structural variants (germline or somatic) from paired-end data. It can process WGS or WES data and supports germline SV calling on one or more samples (<=10) and somatic SV calling for matched tumor-normal pairs or tumor-only data.