Release notes

November 21st, 2022

Recently published apps

We have published the Bracken 2.7 toolkit:

  • Bracken (Bayesian Reestimation of Abundance with KrakEN) tool is used for abundance estimation at the species level, the genus level, or above.
  • Bracken Build is used to prepare the reference database for Bracken.

In addition, Metagenomics Profiling – Kraken2 workflow has been published on the Platform. It is used for metagenomic classification, abundance estimation, and visualization.

We have also published the following tools:

  • FlowSOM 2.4.0 which presents an algorithm used to distinguish cell populations from both flow and mass cytometry data in an unsupervised way.
  • cytofkit2 0.99.80 which is designed to analyze mass cytometry data from FCS files. It includes preprocessing, cell subset detection, cell subset visualization and interpretation, and inference of subset progression.
  • flowAI 1.24.0 which performs quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: flow rate, signal acquisition, and dynamic range, the quality control enables the detection and removal of anomalies.
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November 7th, 2022

Recently published apps

We have recently published the following apps:

  • SBG Single-Cell RNA Deep Learning – Training, a single-cell classifier pipeline for human data. It relies on the transfer learning approach, which uses pre-trained gene embeddings as the starting point for building a model adjusted to given single-cell datasets.
  • SBG Single-Cell RNA Deep Learning – Predict, a single-cell classifier pipeline for human data. This app uses the deep learning model generated by the SBG Single-Cell RNA Deep Learning – Training workflow to classify the input dataset.
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October 31st, 2022

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.
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October 24th, 2022

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).
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August 8th, 2022

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.

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August 1st, 2022

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, a tool which is used for evaluating variant calls.
  • GATK FilterMutectCalls, 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.
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July 25th, 2022

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.
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July 18th, 2022

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.

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June 27th, 2022

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.
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We are always engaged in research and development, working to build the future of genomics, science, and health. Let's work together. We'd love to hear about your projects and challenges, so drop us a line.

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