Fast sequencing data quality metrics

A python package, command-line tool, and Shiny application to compare short tandem repeat (STR) profiles.

The Complete Python Antibody Library

Long read / genome alignment software

My xslt sandbox

Supporting code for the microsatellite genotyping paper introducing CHIIMP

MMseqs2: ultra fast and sensitive search and clustering suite

A Rust CLI to manage your data analysis projects in a streamlined, easy and simple way, getting reproducibility for free.

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and …

fastq2bcl convert fastq files in a bcl2fastq-able run directory.

Tools for annotation, processing and ML for antibody sequences

Tool to build a panel of Y-STRs markers starting from WGS samples and a Y chromosome reference.

T/B cell receptor sequencing analysis notes

C code to validate a fasta file

Sequencing Data for Steichen et al, Science 2019

Data management framework for Python that provides functionality to describe, extract, validate, and transform tabular data

Code and documentation for Simera v2.1.

Efficient evolution from protein language models

Sapiens is a human antibody language model based on BERT.

Ancestral lineage reconstruction using BEAST or RevBayes

VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.

Smith-Waterman alignment for immunoglobulins

R Shiny tool to interactively visualize and analyze antibody repertoires

A Bayesian Phylo-HMM for B cell receptor sequence analysis