Release notes

The Change-O 1.3.0 toolkit is the latest new toolkit addition in our Public Apps gallery. It includes the following apps: 

• DefineClones – assigns Ig sequences into clonal groups. 
• BuildTrees – creates IgPhyML input files. 
• ParseDb – parses and updates input database files. 
• AlignRecords – multiple aligns sequence fields. 
• AssignGenes – assigns V(D)J gene annotations. 
• MakeDb – creates standardized databases output from the input germline alignment results. 
• CreateGermlines – reconstructs germline V(D)J sequences for alignment data. 
• ConvertDb – parses input tab-delimited database files and converts them to different output formats. 

We updated Broad Institute’s best practices for somatic copy number variant discovery analyses, to version 4.2.5.0 in our Public Apps gallery: 

• GATK Somatic CNV Panel Workflow 4.2.5.0 – used for creating a panel of normals (PON) given a set of normal samples. 
• GATK Somatic CNV Pair Workflow 4.2.5.0 – used for detecting copy number variants (CNVs) from WES/WGS single sample data in tumor-only or matched-normal mode. 

The pRESTO 0.7.1. toolkit is the latest new toolkit addition in our Public Apps gallery. It includes the following apps: 

• ParseLog – Parses pRESTO log records and outputs values in TAB-separated tables. 
• BuildConsensus – Builds consensus sequences. 
• ClusterSets – Clusters sequences into groups. 
• CollapseSeq– Removes duplicates sequences from input FASTA/FASTQ files. 
• PairSeq – Sorts and matches sequences across input files. 
• ConvertHeaders – Converts sequence headers to pRESTO format. 
• AlignSets – Aligns sequences using different methods. 
• FilterSeq – Filters input sequences. 
• ParseHeaders – Manipulates sequence headers. 
• SplitSeq – Splits and samples sequence files. 
• UnifyHeaders – Reassigns or deletes sequence header fields. 
• AssemblePairs – Assembles paired-end reads to a single sequence. 
• MaskPrimers – Removes primers and annotates sequences with primers and barcodes. 
• EstimateError – Estimates annotation set error rates.  

We also published the following new tools: 

• ComBat-seq (sva 3.35.2), an R tool used for batch effect adjustment in bulk RNA-seq data. Some additional improvements to the tool wrapper were developed, like removing more than one batch by dataset and adapting outputs to be compatible with downstream analyses (DeSeq). 
• GffRead (0.12.7) GFF/GTF utility tool providing format conversions, filtering, FASTA sequence extraction, and more. 

We published the following updates in our Public Apps gallery: 

• RNA-seq alignment – STAR (2.7.10a), a workflow that performs the first step of RNA-seq analysis – alignment of the reads to a reference genome. It is used to generate aligned BAM files (in genome and transcriptome coordinates) from RNA-seq data, which can later be used in further RNA studies, like gene expression analysis. 
• Trim Galore! (0.6.10) is a wrapper around adapter trimming and quality control tools Cutadapt and FastQC with extra functionality for RRBS data.

Data Browser on the Seven Bridges Platform deprecated to promote interoperability with the CGC  

As the next step in promoting interoperability, we deprecated the Data Browser on the Seven Bridges Platform. As Data Browser remains available on the CGC, this will help promote the CGC as the hub for publicly available data and enable Seven Bridges Platform users who have a CGC account to discover all datasets that are available in the Data Browser on the CGC and much more. 

To complete the process of Data Browser deprecation, in the upcoming period we will disable access to files that were previously imported using Data Browser.  

Recently published apps

 We published Immcantation toolkit 4.4.0 in our Public Apps gallery. The toolkit consists of a set of pipeline scripts which are wrapped as the following tools: 

• preprocess-phix – removes reads which align to phiX174 from the input sequence file. 
• presto-abseq – runs pRESTO tools for pre-processing of NEBNext / ABSeq immune sequencing data. 
• presto-clontech – uses pRESTO tools for analyzing Takara Bio/Clontech SMARTer v1 immune sequencing kit data. 
• presto-clontech-umi – uses pRESTO tools for analyzing Takara Bio/Clontech SMARTer v2 (UMI) immune sequencing kit data. 
• changeo-10x – annotates and infers clonal relationships in Cell Ranger 10x Genomics single-cell V(D)J data. 
• changeo-igblast – does V(D)J alignment using IgBLAST. 
• tigger-genotype – does TIgGER polymorphism detection and genotyping. 
• shazam-threshold – calculates clonal assignment threshold. 
• changeo-clone – runs Change-O cloning and germline reconstruction. 

We also published Nirvana 3.18.1. Nirvana annotates variants from VCF file input and generates a JSON file with results. 

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.