Release notes

Recently published apps

We have published HTSeq-count (2.0.2 in CWL 1.2). HTSeq-count is a Python tool for counting how many reads map to each feature. It takes aligned reads together with a list of genomic features as inputs, and outputs a TSV table with counts for each genomic feature.

We have just published five tools from the GraphicsMagick 1.3.38 toolkit, the swiss army knife of image processing:

• GraphicsMagick compare compares two images using statistics and/or visual differencing. The tool compares two images and reports difference statistics according to specified metrics, and/or outputs an image with a visual representation of the differences.
• GraphicsMagick composite composites (combines) images to create a new image.
• GraphicsMagick conjure interprets and executes scripts in the Magick Scripting Language (MSL). The Magick scripting language (MSL) will primarily benefit those that want to accomplish custom image processing tasks but do not wish to program.
• GraphicsMagick convert is used to convert an input image file using one image format to an output file with the same or different image format while applying an arbitrary number of image transformations.
• GraphicsMagick montage creates a composite image by combining several separate images.

Recently published apps

We have just published two Bowtie2 2.4.5 (CWL 1.2) tools:

• Bowtie2 Indexer, for building a Bowtie index from a set of DNA sequences.
• Bowtie2 Aligner, for performing end-to-end read alignment.

On top of that, there are two more additions to our Public Apps gallery:

• RSeQC – Junction Saturation 5.0.1 (CWL 1.2) tool for determining if the sequencing depth is sufficient to perform alternative splicing.
• GATK IndexFeature 4.2.5.0 tool.

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).