Can Alkan

Somatic structural variation discovery on cancer pangenome graphs

JANUS discovers somatic structural variants in cancer genomes using a pangenome graph approach, achieving high accuracy and efficiency compared to traditional methods.

Toward space-optimal approximate colored indexes at scale

This paper introduces Zindex, a space-efficient indexing framework for large-scale sequence repositories, achieving compact storage and fast query performance with novel interleaved filters and merging mechanisms.

KENT: Fast Pathogen Screening with NVIDIA Jetson Cluster in Resource-Constrained Areas

KENT enables fast metagenomic pathogen screening on low-memory hardware using NVIDIA Jetson Nano clusters, achieving speedups while maintaining accuracy comparable to desktop-based methods.

GenCore: Genomic distance estimation using Locally Consistent Parsing

GenCore uses Locally Consistent Parsing to sketch and estimate genomic distances between closely related large genomes, successfully reconstructing simulated progression trees and recapitulating primate phylogeny.

Rapid Adaptive Increase of Amylase Gene Copy Number in Indigenous Andeans

The paper identifies a rapid adaptive increase in AMY1 gene copy number in Indigenous Peruvian Andeans linked to potato domestication.

FASTR: Reimagining FASTQ via Compact Image-inspired Representation

FASTR is a new format for storing sequencing data that reduces file size and improves processing speed compared to FASTQ.

Robust software development practices improve citations of RNA-seq tools

This study shows that better software development practices for RNA-seq tools lead to more citations, as evidenced by a strong statistical association between development quality and citation counts.

Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome data

This paper compares methods to reduce reference bias and postmortem damage in ancient genome data, finding that graph alignment and bamRefine improve accuracy and genotyped loci.

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering

TargetCall filters out off-target reads before basecalling to reduce computational waste, improving basecalling performance and efficiency.

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes

AirLift remaps reads from one reference genome to another efficiently and accurately, reducing execution time by up to 27.4x compared to full mapping.

ECOLE: Learning to call copy number variants on whole exome sequencing data

ECOLE is a deep learning model for detecting copy number variants in whole exome sequencing data, achieving improved precision and recall over existing methods.

BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis

BLEND improves genomic sequence analysis by efficiently finding fuzzy seed matches, enhancing speed, memory use, and accuracy in read overlapping and mapping.

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

CONGA genotypes copy number variants in ancient genomes and low-coverage data, showing coherent deletion frequencies and purifying selection across 50 ancient human genomes.

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

Polishing Copy Number Variant Calls on Exome Sequencing Data via Deep Learning

DECoNT improves CNV detection accuracy on WES data by learning from matched WES and WGS data, tripling duplication precision and doubling deletion precision.

Characterization of segmental duplications and large inversions using Linked-Reads

The paper introduces VALOR2, a new software package that uses Linked-Read sequencing to detect large genomic inversions and characterize interspersed segmental duplications.

A robust benchmark for germline structural variant detection

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

The paper develops TARDIS, a tool for accurately detecting complex structural variations, including tandem and interspersed segmental duplications, using short-read whole genome sequencing data.

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Hercules corrects long read errors using a profile HMM-based machine learning approach, achieving high mapping rates and accuracy when short reads cover most of the long reads.

Discovery of large genomic inversions using pooled clone sequencing

The paper introduces dipSeq, an algorithm for discovering large genomic inversions using pooled clone sequencing, validated on simulated and real data.

LEAP: A Generalization Of The Landau-Vishkin Algorithm With Custom Gap Penalties

The paper introduces LEAP, a generalized algorithm for approximate string matching that outperforms existing methods in speed under various scoring schemes.

Computational Pan-Genomics: Status, Promises and Challenges

This paper reviews computational pan-genomics, discussing its status, potential, and challenges across multiple biological disciplines.