Recently published apps

The following apps were published in CWL1.x:

• Single Cell Multi Sample Pairwise Differential Expression Workflow – pipeline that performs differential expression analysis on single cell data between pairs of user defined conditions.
• Minimap2 v2.17 – a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database, tailored for use with long read sequencing technologies.
• fastqValidator 0.1.1 – checks format correctness of paired-end and single-end FASTQ files.
• FastP 0.20.1 – ultra-fast FASTQ preprocessor with useful quality control and data-filtering features, including adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of FASTQ data.
• SBG convert SRA/BAM to FASTQ – an all-in-one tool that converts SRA/SAM/BAM/CRAM files into FASTQ format.
• SBG Create Expression Matrix – creates aggregated matrices from various types of inputs, most typically from abundance estimates produced by tools like RSEM, Salmon, or Kallisto.
• SHAPEIT 4.2.1 – phasing tool for sequencing and SNP array data.
• Regenie 2.0.1 – tool for whole genome regression analysis.
• UMI-tools 1.1.1 – tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.

Marko Marinkovic