Release notes

Recently published apps

We published the following apps in our Public Apps gallery:

• RNA-SeQC 2.4.2, a tool that computes post-alignment quality control metrics for RNA-Seq data. It takes aligned reads in BAM/SAM or CRAM format and an annotation file as inputs, and outputs different alignment metrics files
• scCODA 0.1.9, a Python-based tool that performs differential analysis of cell populations.

Recently published apps

We have just published the following tools from the BBTools 39.01 toolkit:

• BBDuk: used for trimming, filtering, and masking of input reads.
• Reformat: used for generic read-processing tasks (changing ASCII quality encoding, interleaving, file format, compression).
• BBMap: used for splice-aware read alignment.
• Dedupe: used for removing duplicates from input sequences.
• SplitNextera: used for splitting Nextera long-mate-pair reads.
• CalcUniqueness: used for determining library complexity and the need for additional sequencing by generating kmer uniqueness histogram.
• Taxonomy: used for printing taxonomy information for provided organism identifiers.
• Repair: used to correct disordered reads and reads whose mates have been lost.
• Seal: used for alignment-free sequence quantification.
• BBMerge: used for merging overlapping paired end reads.
• BBMask: used for masking low-complexity, tandem repeats or SAM mapped regions.
• Tadpole: used as a kmer-based assembler.
• Statistics: used for calculating assembly statistics.
• BBNorm: used for normalizing read depth based on kmer counts.

NewDRS notification improvements and the brand new Activity center

To provide you with more detailed information about each DRS import operation and enable you to resolve import issues independently, we have improved DRS-related notifications and implemented the Activity center, available by clicking Open activity center in the Activity feed. When any of the items from a particular DRS import fail, you will be able to see an error message and a corresponding error code for each of the items, allowing you to understand and try to fix the issue. Furthermore, a description and link to the relevant documentation will be provided for each import from a DRS server.

Recently published apps

We have just published RTG Tools 3.12.1 (ROCPlot, VCFEval, Format), MaxQuant 2.4.2.0 and GATK GenotypeGVCFs 4.4.0.0 tools:

• RTG Tools Format converts data files from FASTA/FASTQ/SAM/BAM into the RTG Sequence Data File (SDF) format.
• RTG Tools VCFEval is a tool that performs sophisticated comparison of VCF files.
• RTG Tools ROCPlot is used to plot ROC curves from ROC data files generated by RTG Tools VCFEval.
• MaxQuant integrates algorithms specifically developed for high-resolution, quantitative MS data, and it is applicable for shotgun proteomics.
• GATK GenotypeGVCFs is used to joint-genotype GVCF files created by GATK HaplotypeCaller/GATK GenomicsDBImport tools.

Recently published apps

We published Giraffe-DeepVariant workflow 1.0, Cramino 0.9.7 and kyber 0.4.0 tools from the NanoPack2 toolkit, as well as Pisces 5.3.0.0 tool, PureCN NormalDB workflow 2.6.4, PureCN workflow 2.6.4, zUMIs 2.9.7 tool, and AlphaFold 2.3.2 tool. Here are the details:

• Giraffe-DeepVariant workflow 1.0 is a pipeline for calling small variants using the pangenome reference. The workflow starts with sequenced reads (FASTQs, CRAM). Reads are mapped to a pangenome with vg giraffe and pre-processed (e.g. indel realignment) before performing the variant calling step using DeepVariant.
• Cramino 0.9.7 is a quick QC tool intended for long-read sequencing. It takes a BAM/CRAM format alignment file and creates a QC report with mean coverage, number of reads, their mean and median length and sequence identity relative to the reference genome.
• kyber 0.4.0 creates a 600×600 pixel heatmap image of read length and read accuracy from input alignment file (BAM/CRAM format).
• Pisces 5.3.0.0 does variant calling from aligned amplicon sequencing data.
• PureCN NormalDB workflow 2.6.4 builds a normal database which is used for coverage normalization in PureCN workflow.
• PureCN workflow 2.6.4 estimates tumor purity and ploidy, copy number and loss of heterozygosity (LOH). Calculated purity and ploidy combinations are sorted by likelihood score. Copy number and LOH data are provided by both gene and genomic region. The steps in the workflow include: preparation of an interval file for further analysis, calculation of coverage for tumor and normal samples (optionally for additional tumors) and final calculation of purity, ploidy, copy number and LOH results.
• zUMIs 2.9.7 takes RNA-seq data with or without UMIs, STAR index files archive and annotation GTF file and analyzes the data as specified by the other input parameters.
• AlphaFold 2.3.2 is a machine-learning application which incorporates knowledge about physical and biological protein structure properties into a deep learning algorithm, and predicts protein structures with high accuracy.

Recently published apps

We published the following apps in our Public Apps gallery:

• RADx-rad v0.2 Workflow, which is used for metagenomic data analysis of SARS-CoV-2 from wastewater samples. The workflow was developed and ported to CWL as a part of the RADx (Rapid Acceleration of Diagnostics) – the initiative to speed innovation in the development, commercialization, and implementation of technologies for COVID-19 testing, launched by The US National Institutes of Health (NIH).
• CNVPanelizer 1.32.0, which generates a report table and visualization of detected CNVs from targeted sequencing data.
• Control-FREEC 11.6 which can be used for somatic copy number analysis of WGS, WES and targeted data.

DRS import available on the Seven Bridges Platform

With the introduction of DRS import on the Seven Bridges Platform, you are now able to import files from either external sources or the Cancer Genomics Cloud (CGC). This also presents a significant improvement to data interoperability, as CGC users who have adequate authorizations can now successfully access CGC datasets from the Platform using DRS import. Imported files can then be used as any other file on the Platform.

Learn more about DRS import.

Recently published apps

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

• VEP Slivar Trios Rare Diseases Analysis with VEP 109.3 version and Slivar 0.3.0 version inside. This analysis is used for preprocessing and analyzing variants from related individuals (trios or families; WES or WGS).
• STAR-Fusion (v1.12.0), an app that uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads.
• STAR-Fusion Build FusionFilter Dataset (v1.12.0) that creates the required CTAT genome lib archive for STAR-Fusion execution.
• Cutadapt (v4.4), an app most commonly used for removing adapter sequences. It finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequences from high-throughput sequencing reads.
• Seven tools from the Kalisto 0.48.0 toolkit:
  • kallisto quant computes equivalence classes for reads and quantifies transcript abundances from RNA-Seq data.
  • kallisto quant-tcc runs the EM algorithm on a supplied TCC matrix file to make transcript-level estimates.
  • kallisto bus produces BUS (Barcode-UMI-Set format) output files from single-cell RNA Seq datasets.
  • kallisto merge merges the results of several batches obtained by kallisto pseudo.
  • kallisto h5dump converts HDF-5-formatted results to plaintext.
  • kallisto index builds an index from a transcriptome FASTA formatted file of target sequences.
  • kallisto inspect outputs the target de Bruijn Graph from the kallisto index file in different file formats.

Recently published apps

We published the following apps in our Public Apps gallery:

• Parabricks fq2bam (4.0.0-1) – GPU-accelerated alignment, duplicate marking and optionally BQSR.
• Parabricks haplotypecaller (4.0.0-1) – GPU-accelerated GATK HaplotypeCaller.
• Parabricks deepvariant (4.0.0-1) – GPU-accelerated version of DeepVariant.
• Parabricks Somatic Calling workflow – calling somatic variants from a matched tumor-normal sample pair. It is based on running accelerated Mutect2 on GPU instances with or without a panel of normals.