ParseLog.py

toolkit for processing B and T cell sequences

Install

All systems
curl cmd.cat/ParseLog.py.sh
Debian Debian
apt-get install python3-presto
Ubuntu
apt-get install python3-presto
image/svg+xml Kali Linux
apt-get install python3-presto
Windows (WSL2)
sudo apt-get update sudo apt-get install python3-presto
Dockerfile
dockerfile.run/ParseLog.py

python3-presto

toolkit for processing B and T cell sequences

pRESTO is a toolkit for processing raw reads from high-throughput sequencing of B cell and T cell repertoires. Dramatic improvements in high-throughput sequencing technologies now enable large-scale characterization of lymphocyte repertoires, defined as the collection of trans-membrane antigen-receptor proteins located on the surface of B cells and T cells. The REpertoire Sequencing TOolkit (pRESTO) is composed of a suite of utilities to handle all stages of sequence processing prior to germline segment assignment. pRESTO is designed to handle either single reads or paired-end reads. It includes features for quality control, primer masking, annotation of reads with sequence embedded barcodes, generation of unique molecular identifier (UMI) consensus sequences, assembly of paired-end reads and identification of duplicate sequences. Numerous options for sequence sorting, sampling and conversion operations are also included.