Tools and services developed by cATG

Several tools and services have been developed, which are publicly available for use by anyone:

Pipeline SARS-CoV-2
  • Pipeline developed in Nextflow designed for assembling SARS-CoV-2 samples sequenced with Oxford Nanopore platforms.
  • Includes the following processes:
    • Basecalling and demultiplexing (optional)
    • Assembly and variant calling
    • Variant annotation
    • Identification of clades and lineages
    • Quality metrics and statistics.
    • Summary in Excel format (with all relevant information)
    • Initial report for data submission to GISAID

Available at: https://github.com/catg-umag/ncov2019-ont-nf

Mutational signatures
  • Pipeline for extracting mutational signatures and their general characterization.
  • Includes the following processes:
    • Creation of a list of mutations (optional)
    • Collection of additional information on variants (context, AID reason, SNV at IG locus)
    • Extraction of SBS signatures
    • Adjustment using COSMIC signatures
    • Reconstruction of signatures
    • Report with all obtained graphics
  • As a result, a CSV file is produced with all the mutations found, along with various files associated with the mutational signatures extracted from the samples.

Available at: https://github.com/catg-umag/bcell-lymphomas-mutational-signatures

AID Mutations
  • Visualization of mutations in selected genes in human and mouse genomes, highlighting whether there is occurrence in patterns associated with AID contexts.

Available at: https://catg.cl/lab/tools/aid-mutations/

Peptipedia
  • Peptipedia is a computational platform designed to support the study of peptides and their properties. It hosts the largest database of biologically active peptides reported to date, with approximately 100,000 sequences. This tool characterizes peptides from various perspectives, including physicochemical properties, phylogenetic, and functional attributes. Additionally, it offers a range of computational services for sequence analysis, such as predicting physicochemical properties, phylogenetic and functional characterization, and predictive methods for classifying biological activities. Various computational tools based on machine learning methods have been integrated to facilitate the training of predictive models and pattern identification, promoting the use of such technologies in biotechnological and industrial applications. Currently, work is underway on the second version of the platform, incorporating methods for predicting interactions with T cells and studying promiscuity, as well as developing peptide design rules using deep generative models.

Available at: https://peptipedia.cl

Additionally, the following services are available:

Genomic analysis
  • Sanger sequencing
  • NGS sequencing
  • Metabarcoding
  • Nucleic acid quality control service.
  • 16S bacteriome
  • Fungal analysis by ITS and 18S
  • Molecular diagnostic services
  • Bioinformatic design and analysis with customized pipelines
  • Genomic surveillance
  • Coming soon: Environmental DNA analysis

Contact: [email protected]