Chirag Jain

This paper introduces a rigorous framework for haplotype-aware long-read error correction, achieving accuracy comparable to existing methods in de novo contexts.

NanoLabel improves real-time nanopore signal classification by accelerating the workflow and enhancing accuracy using a lightweight classifier and data augmentation.

The paper presents a comprehensive genomic atlas of Indian populations, identifying novel variants and highlighting genetic diversity and pharmacogenomic implications.

The paper introduces an integer programming framework for haplotype-resolved genotyping using pangenome graphs, achieving accurate MHC haplotype inference on low-coverage data.

The paper introduces RAFT, an assembly algorithm that reduces gaps in telomere-to-telomere genomes by managing contained reads, showing improved performance on real datasets.

This paper develops haplotype-aware sequence alignment algorithms for pangenome graphs, showing improved consistency with ground-truth recombinations compared to haplotype-agnostic methods.

The paper presents an exact algorithm for co-linear chaining on cyclic pangenome graphs, demonstrating improved accuracy over heuristic methods in aligning simulated long reads.

The paper develops a theoretical framework to analyze coverage-preserving properties of graph models for long-read assembly and proposes heuristics to avoid coverage gaps.

The paper develops a new chaining algorithm for aligning long reads to pangenome DAGs, achieving high precision with low unmapped reads.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

This paper introduces Winnowmap2, a long read mapping method that reduces allelic bias in repetitive sequences, improving variant calling accuracy in near-identical repeats.

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

This paper presents efficient algorithms for co-linear chaining with anchor overlaps and gap costs, showing strong correlation with edit distance.

The paper optimizes minimap2 for faster long-read mapping on CPUs, achieving up to 1.8x speedup without changing output.

The paper introduces a variant selection framework to reduce variation graph size while preserving paths with limited differences, achieving significant graph reduction in human chromosome 1.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

The paper introduces a weighted minimizer sampling algorithm to improve long-read mapping accuracy, particularly in repetitive regions, by reducing false positives while maintaining match guarantees.

MetaMaps assigns long-read metagenomic sequences to species and estimates sample composition with high accuracy and scalability.

FastANI accurately estimates average nucleotide identity (ANI) up to 782-fold faster than BLAST; across 90K prokaryotic genomes, an 83-95% ANI gap supports a 95% species boundary.

The paper introduces a fast algorithm for computing whole-genome homology maps, achieving efficient alignment with high accuracy and coverage.

The paper introduces a fast approximate algorithm for mapping long reads to large reference databases, achieving high speed and precision by combining minimizers with MinHash identity estimation.