Recently published apps

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

• Mosdepth 0.3.3 toolkit: Mosdepth, a tool used for fast depth calculation on WGS, WES or targeted BAM and CRAM files and Mosdepth plot_dist which plots Mosdepth results.
• Personal Cancer Genome Reporter 1.0.3 which is used for functional annotation and classification of somatic variants.
• Cancer Predisposition Sequencing Reporter 1.0.0 which analyzes cancer-predisposing germline variants.

We have also updated versions and published tools from the following two toolkits: SRA (v3.0.0, CWL1.2) and Salmon (v1.5.2, CWL1.2). Tools that got the update are:

• SRA sam-dump that converts SRA data into SAM format. With aligned data, NCBI uses Compression by Reference, which only stores the differences in base pairs between sequence data and the segment it aligns to. The process to restore original data, for example as FASTQ, requires fast access to the reference sequences that the original data was aligned to.
• SRA fasterq-dump that converts SRA data into FASTQ format while using temporary files and multi-threading to speed up the extraction.
• SRA fastq-dump that converts SRA data into FASTQ format.
• Salmon Alevin that introduces a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data.
• Salmon Index that builds an index necessary for the Salmon Quant and Salmon Alevin tools. To create an index, it uses a transcriptome reference file in FASTA format. Additionally, one can provide a genome reference along with the transcriptome to create a hybrid index compatible with the improved mapping algorithm named Selective Alignment.

Marko Marinkovic