Mahmudur Rahman Hera

Estimation of substitution and indel rates via k-mer statistics

Mahmudur Rahman Hera, Paul Medvedev, David Koslicki, Antonio Blanca

Abstract Methods utilizing $$k$$ k -mers are widely used in bioinformatics, yet our understanding of their statistical properties under realistic mutation models remains incomplete. Previously, substitution-only mutation models have been considered to derive precise expectations and variances for mutated $$k$$ k -mers …

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YACHT: Software for an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample

Maksym Lupei, Shaopeng Liu, Chunyu Ma, Adam Park et autres

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YACHT: Software for an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample

Maksym Lupei, Shaopeng Liu, Chunyu Ma, Adam Park et autres

yacht-1.3.2.tar.gz, upload for JOSS publication includes source code

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YACHT: Software for an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample

Maksym Lupei, Shaopeng Liu, Chunyu Ma, Adam Park et autres

yacht-1.3.2.tar.gz, upload for JOSS publication includes source code

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MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements

Mahmudur Rahman Hera, David Koslicki, Conrado Martı́nez

Abstract With the surge in sequencing data generated from an ever-expanding range of biological studies, designing scalable computational techniques has become essential. One effective strategy to enable large-scale computation is to split long DNA or protein sequences into k -mers, and summarize …

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Leveraging FracMinHash Containment for Genomic d N / d S

Judith Rodríguez, Mahmudur Rahman Hera, David Koslicki

Abstract Increasing availability of genomic data demands algorithmic approaches that can efficiently and accurately conduct downstream genomic analyses. These analyses, such as evaluating selection pressures within and across genomes, can reveal developmental and environmental pressures. One such commonly used metric to measure …

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Estimating similarity and distance using FracMinHash

Mahmudur Rahman Hera, David Koslicki

MOTIVATION: -mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash has emerged as a popular sketching technique and has been used in several useful applications. Recent studies on FracMinHash proved unbiased estimators for the …

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sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets

Luiz Irber, N. Tessa Pierce‐Ward, Mohamed Abuelanin, Harriet Alexander et autres

Irber et al., (2024). sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. Journal of Open Source Software, 9(98), 6830, https://doi.org/10.21105/joss.06830

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Metagenomic functional profiling: to sketch or not to sketch?

Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith Rodríguez et autres

MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against …

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Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation

Mahmudur Rahman Hera, David Koslicki

Abstract Motivation The increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizing k -mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash …

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Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches

Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith Rodríguez et autres

Motivation: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against …

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Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash

Mahmudur Rahman Hera, N. Tessa Pierce‐Ward, David Koslicki

Sketching methods offer computational biologists scalable techniques to analyze data sets that continue to grow in size. MinHash is one such technique to estimate set similarity that has enjoyed recent broad application. However, traditional MinHash has previously been shown to perform poorly …

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