Release notes

Recently published apps

We have just published the following three tools:

• SPAdes 3.15.5 – an assembly tool containing various assembly pipelines. SPAdes can be used for reads produced by different sequencing technologies, such as: Illumina, IonTorrent, PacBio, Oxford Nanopore and Sanger. SPAdes was tested on small genomes (eg. bacterial, fungal) and is not intended for larger ones.
• Unicycler 0.5.0 – a tool for bacterial genome assembly. It can assemble Illumina-sequenced reads, as well as PacBio or Nanopore long-read-only sets (for the best assemblies, it can conduct a hybrid assembly by taking both Illumina and long reads).
• Quast 5.2.0 – a tool for genome assembly evaluation. QUAST implements different methods for analyzing assemblies. By default, it utilizes Minimap2 for alignment. GeneMarkS, GeneMark-ES, Glimmer, Barrnap and BUSCO are used for gene prediction, while finding structural variations is done by BWA, Sambamba, and GRIDSS. Additionally, QUAST uses bedtools for calculating read coverage, which is presented in the Icarus contig alignment viewer.

Recently published apps

We have published six tools from the BEDTools 2.30.0 toolkit:

• BEDTools Coverage – returns the depth and breadth of coverage of features from B on the intervals in A.
• BEDTools Genomecov – computes histograms of feature coverage for a given genome.
• BEDTools GetFasta – extracts sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.
• BEDTools Intersect – screens for overlaps between two sets of genomic features.
• BEDTools Merge – combines overlapping or “book-ended” features in an interval file into a single feature.
• BEDTools Sort – sorts a feature file by chromosome and other criteria.

We have also published the Functional Equivalence Evaluation workflow for comparing the functional equivalence of different WGS/WES processing analyses. Functional Equivalence Evaluation workflow is used to establish if the results can be used together (compared, merged) in downstream analyses (common scenario with large, multi-center sequencing studies where different institutions use their own analysis protocols) or considered equally valid for drawing conclusions.

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.

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.

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.