Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 500 universities from 70 countries including Stanford, MIT, Harvard, and Cambridge.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Tools (written in C using htslib) for manipulating next-generation sequencing data

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Python Lex-Yacc

calling SVs from Blasr contig level alignments