Sam Kovaka

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

Sigmoni: classification of nanopore signal with a compressed pangenome index

Sigmoni classifies nanopore signals using a compressed pangenome index, enabling efficient and accurate classification of reads against large references.

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

MEM-based pangenome indexing for k-mer queries

The paper introduces MEMO, a pangenome indexing method that efficiently handles k-mer queries and conservation analysis across pangenomes.

High resolution copy number inference in cancer using short-molecule nanopore sequencing

This paper demonstrates that sequencing short DNA molecules with nanopore sequencing improves copy number inference in cancer, offering higher sensitivity and accuracy compared to traditional methods.

Pan-genomic Matching Statistics for Targeted Nanopore Sequencing

SPUMONI enables fast and accurate targeted nanopore sequencing using efficient pangenome indexes, outperforming minimap2 in speed and memory usage.

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

UNCALLED enables real-time targeted nanopore sequencing by mapping raw electrical signals to references, improving coverage and variant detection in bacterial and human genomes.

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

StringTie2 assembles error-prone long reads, recovering on average 8.3 and 2.6 times as many correct transcripts as FLAIR and Traphlor, and outperforms Scallop on short reads.