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Metagenomics

• New Taxonomic Classifications via Silva, Greengene and GTDB

Single Cell Transcriptomics

•  Improved UMAP Performance for Large Datasets

Long Read Transcriptomics

• New Feature to Combine Transcriptomes with TAMA Merge
• Redesigned PacBio IsoSeq Pipeline

Transcriptomics

• Improved Time Course Data Analysis with Masigpro
• Improved Differential Expression Analysis Gene Filtering
• New Feature: Batch Renaming of Feature IDs for Count Tables and Differential Expression Results
• New Feature: Renaming and Deleting of Samples for Count Tables

Genome Analysis

• New Feature: Genome Assembly Completeness Assessment with Busco

General

• New Info Icon in all tabs to view analysis details

Single Cell Transcriptomics

• New: Cell Type Identification with SingleR
• Update: Interactive Single-Cell Visualization and Annotation Tool
• Update: Seurat v.5 – Update: Improved Trajectory Analysis with Monocle
• New: Autocorrelation Analysis via Monocle3

Long Read Transcriptomics

• New: Isoform Definition and Quantification with IsoQuant
• New: Reference-Free Long-Read Transcriptome with isON pipeline
• Update: FLAIR v.2 including Quantification
• Update: Curation of Long-Read Transcriptomes with SQANTI3 v.5

Transcriptomics

• Update: Busco Database – Update: EdgeR v.4
• Improved Gene-Level Quantification with HTSeq Count (now cloud based)

Genetic Variation

• New: Merge and Extract VCF Files
• New: Population Structure Analysis with ADMIXTURE
• New: Imputation and Phasing with Beagle
• New: Filtering for GBS data via dDocent Pipeline

Genome Analysis

• Update: Evidence-based eukaryotic gene predictions with Augustus

Functional Analysis

• New: Find Pathways via Annotations

General

• Improved Trimmomatic Wizard (now cloud based)
• Improved Application Messages
• OmicsBox now available for macOS ARM architecture

Functional Analysis

• Removed MobiDB-Lite from InterProScan due to the lack of GO information

Genetic Variation

• Fixed Issue when Saving MAGMA Objects

Transcriptomics

• Fixed GTF/GFF Input for STAR
• Fixed Issue for Cell-Barcoded and Full-Length Modality in STARsolo
• Fixed Single-cell Dimensionality Check for Count Matrix Import
• Improved STARsolo Chart for Genes Distributions in Percentages

Metagenomics

• Fixed Pairing Factor Issue of the Differential Taxonomic Abundance Analysis.

General

• More Specific Task Error Messages

• New Bubble Plot for GSEA
• Updated GO-Slim Links
• Fixed GO Annotation Taxa Filtering

• Added Single-Cell Count Matrix Dimension Check for MTX Format
• Improved Single-Cell Quantification Summary Report
• Fixed Bug in the STARsolo Wizard
• Changed maSigPro to apply a Negative Binomial Distribution
• Fixed Numeric x-Axis for maSigPro Expression Profiles

• Updated Pfam2GO Links

• Fixed Variant Annotation for Poliploides

• Improved File-Upload Resilience for CloudFiles
• Minor CloudFiles Improvements

Transcriptomics

• New Single Cell RNA-Seq Quantification Feature with StarSolo
• Improved Single Cell RNA-Seq Clustering with Interactive UMAPs
• Improved Single Cell RNA-Seq Trajectory Visualizations: Gene Trends and Expression UMAPS
• New Long-Read Aligner: Minimap2

Genetic Variation

• New Functional Analysis of GWAS Results with MAGMA
• New Variant Calling Option for Mixed-ploidy in Freebayes
• New feature to extract variant information from Variant Annotation using Manhattan Plots

General

• Improved Barcode Demultiplexing Supporting Paired-Ends
• Improved Job Progress and Status Messages
• Improved Proxy Configuration and Authentication

Metagenomics

• Custom Kraken DB Option for Taxonomic Classifications

Functional Analysis

• Custom Diamond Blast DB Option

Genetic Variation Module

• Fast Variant Calling with BCFtools and FreeBayes
• Variant Filtering
• Variant Annotation with Variant Effect Predictor (VEP)
• Guided Genome Wide Association Study

Transcriptomics

• Isoform Definition and Correction with Flair

Functional Analysis 

• Faster Functional Annotation with Diamond Blast
•  KEGG Pathways Analysis for commercial customers

Genome Analysis

• Genome Assembly Comparision and Qualitiy Assessment with QUAST

General Tools

• Barcode Demultiplexing with Cutadapt

General Improvements

• Redesigned Functional Enrichment Analysis Options throughout OmicsBox
• Improved Message Handling for Cloud Jobs
• Option to share Cloud Files

General Tools

• New Tool for the quality control of Long Read DNA-Seq Data
• New Tool for the quality control of RNA-Seq BAM Files
• New option to merge FastA/Q Files

Transcriptomics Module

• Long Read RNA-Seq Quality Control and Filtering with Squanti3
• Single Cell RNA-Seq Differential Expression Analysis including Functional Enrichment
• Single Cell RNA-Seq Trajectory Inference

General Improvements

• Restructuring of Menus and Side Panel Options for improved usability
• Introduction of CloudStorage
• Improved Workflows

Transcriptomics Module

• New Heatmap and PCA 2D/3D Plots
• New Single Cell Clustering Option
• Coding Potential Assesment now part of the Transcriptomics Module

Genome Analysis Module

• MLST feature as part the Genome Analysis Module
• Genome Browser now part of the Genome Analysis Module

Functional Analysis

• Plant Reactome Database for Combined Pathway Analysis
• New Pathway Analysis Charts
• Subcellular Localization Prediction with Psortb

Functional Analysis

• Combined Pathway Analysis

Transcriptomics Module

• De-novo Isoform Discovery for PacBio Long Reads (Iso-Seq)
• Updates for Trinity (2.12.0), BUSCO (5.1.2) and STAR (2.7.8a)

Metagenomics Module

• rRNA Removal with SortMeRNA
• Contaminant Removal with Bowtie2
• Kraken and Pfam (v.34.0) Database Updates

Genome Analysis Module

• New DNA-Seq Alignment with Bowtie 2
• Improved Eukaryotic Gene Finding with Augustus
• Updates for ABySS (2.3.0), SPAdes (3.15.2), Flye (2.8.2), Augustus (3.4.0) and RepeatMasker

General Tools and Improvements

• User Authentication with Account Management
• More interactive charts
• New BAM Tool: Convert BAM to FASTA/Q

Metagenomics Module

• Taxonomic Classification: Kraken2 database update and new parameters
• Taxonomic Classification: New option to add, remove and rename samples
• Taxonomic Classification: Improvements to bar chart

Transcriptomics Module

• RNA-Seq de novo Assembly: Trinity update (v2.10.0), improved performance and new parameters
• GSEA for Pairwise DEA: Ranking is now based on p-values instead of the FDR
• RNA-Seq Alignment: STAR update (v.2.7.5a) and new reference fasta file format (.gz)
• RNA-Seq Alignment: New parameter to include Read Group (@RG) header and tags in BAM output
• Create Count Table Transcript-Level: RSEM update (v.1.3.3)

Genome Analysis Module

• DNA-Seq Polishing: Improved performance due to parallelized analysis
• DNA-Seq Alignment: New reference fasta file format (.gz)
• DNA-Seq Alignment: New parameter to include Read Group (@RG) header and tags in BAM output
• DNA-Seq Assembly (Flye): Flye Update (v.2.8) and support of PacBio HiFi data
• MLST: Database update and wizard improvements

Functional Analysis

• BLAST: New feature “Custom DB Cloud Blast” to run blast against own fasta file

General

• Genome Browser: New reference fasta file format (.gz)

• File Manager: Fixed issue with “Merge Objects”
• Make Blast DB Fix: Internal parameter for win64: BLASTDB_LMDB_MAP_SIZE
• Fisher’s Exact Test: Fixed dialog link and GO selection
• Taxonomic Classification: Improve memory management and improved report formatting
• BWA: Improved name for BAM file output
• Genome Browser: Fixed issue with region selection while scrolling
• FASTQ Preprocessing: Fixed workflow permissions

• Differential Abundance Analysis of Functions and Pathways (EggNOG and Pfam)
• Taxonomic Classification with Kraken: Update to v.2

• RNA-Seq Alignment with BWA
• Sequence Clustering with CD-HIT
• Trinity accepts FASTA read files as input
• Completeness Assessment with BUSCO: Update to v.4 and OrthoDB v.10

• Long-Read De-Novo Assembly and Polishing with Flye and Pilon
• DNA-Seq Alignment with BWA
• DNA-Seq De-Novo Assembly SPAdes: Update to v.3.14

• Filter Fasta by Length
• Convert FastQ to Fasta
• Improved Venn Diagram

Metagenomics Module

• New Taxonomic Classification Statistics: Chao1 OTU Diversity, Rarefaction Curves and PCoA Plot
• OTU Differential Abundance Testing with edgeR

Transcriptomics Module

• Completeness Assessment with BUSCO
• Predict Coding Regions with TransDecoder
• Improved RNA-Seq Alignment Input: GFF is automatically converted to GTF
• New RNA-Seq Alignment Options: 2-Pass mode, Export Spliced Junctions, Export Unmapped Reads
• New RNA-Seq De Novo Assembly Option: SuperTranscripts
• Export Normalised Counts of TimeCourse Results
• Export Normalised Counts of Pairwise Differential Expression Without Replicates Results

Genome Analysis Module

• De-Novo Assembly with SPAdes
• Repeat Masking Database Update DFAM v.3
• Repeat Masking Compatibility with RepBase 2017 and 2018
• Improved Wizard for Sample Selection

General Tools

• Barcode Splitter Tool
• New Example Workflows

General

• Minor visual improvements

Transcriptomics Module

• Create Count Table (Gene-level): Memory usage improvements
• Differential Expression Analysis: Heatmap minor improvements
• RNA-Seq Alignment: Fix bug with fastq files

Metagenomics Module

• Taxonomy Classification: Fix report

• GO Graphs: new option to export the visible region
• Generic Export: new options for start/end query and HSP positions in BlastHits
• Table Viewer: fix scroll issue causing hidden bottom rows
• License: fix the restart loop when using limited mode after key expired
• Blast Results: fix tooltip
• Genome Browser: fix a specific region position issue
• CloudBlast: skip sequences longer than 100k symbols
• Create Count Table: fix download BAM files issue when “Generate Alignment Files” is selected

General

• Fix minor issue regarding citations in wizards

Metagenomics Module

• Fix bug in metagenomics workflows causing tasks to fail

Functional Analysis Module

• Make Blast DB: Taxonomy Map file can be plain text

General

• Allow opening OmicsBox in viewer mode when offline
• Fix: Welcome window sometimes not showing content on MacOS
• Fix: Update previously installed Apps on platform update
• Improvement: Check fastq.gz files for corruption

Transcriptomics Module

• RNA-Seq De Novo Assembly: two additional parameters
• RNA-Seq Alignments: fix output BAM files name
• Differential Expression: improve files parser to skip headers

Genome Analysis Module

• Repeat Masking: unknown species are rejected by the validator

Metagenomics Module

• Fixed problem with white spaces in filenames
• Updated Kraken database to 2019.06
• Improves Krona viewer styling

Functional Analysis Module

• InterProScan: remove deprecated ProDom search option
• Rfam: fix ‘end’ column not showing data

General

• Improved citations in wizards and reports
• Example Data Import option

Transcriptomics Module

• RNA-Seq Alignment against reference genome (STAR)

Genome Analysis Module

• DNA-Seq De Novo Assembly (ABySS 2.0)
• Repeat Masking (RepeatMasker)

Metagenomics Module

• Taxonomic Classification (Kraken)
• Metagenomic Assembly (MEGAHIT and meta-SPAdes)
• Metagenomic Gene Prediction (FragGeneScan and Prodigal)

Functional Analysis Module

• New CloudBlast taxonomy filtering
• Improved CloudIPS speed and resource usage
• New EC class (7)

Jan. 2019

• Blast2GO is now OmicsBox
• Search box for menu actions
• New menu structured by modules
• Bug fixes and improvements
• New Module: Metagenomics