Release notes

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.