Starcode: sequence clustering based on all-pairs search
Motivation: The increasing throughput of sequencing technologies offers new applications
and challenges for computational biology. In many of those applications, sequencing errors …
and challenges for computational biology. In many of those applications, sequencing errors …
MeShClust: an intelligent tool for clustering DNA sequences
Sequence clustering is a fundamental step in analyzing DNA sequences. Widely-used
software tools for sequence clustering utilize greedy approaches that are not guaranteed to …
software tools for sequence clustering utilize greedy approaches that are not guaranteed to …
Bartender: a fast and accurate clustering algorithm to count barcode reads
Motivation Barcode sequencing (bar-seq) is a high-throughput, and cost effective method to
assay large numbers of cell lineages or genotypes in complex cell pools. Because of its …
assay large numbers of cell lineages or genotypes in complex cell pools. Because of its …
Defining loci in restriction‐based reduced representation genomic data from nonmodel species: Sources of bias and diagnostics for optimal clustering
Next generation sequencing holds great promise for applications of phylogeography,
landscape genetics, and population genomics in wild populations of nonmodel species, but …
landscape genetics, and population genomics in wild populations of nonmodel species, but …
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Motivation: The innovation of restriction-site associated DNA sequencing (RAD-seq) method
takes full advantage of next-generation sequencing technology. By clustering paired-end …
takes full advantage of next-generation sequencing technology. By clustering paired-end …
De novo clustering of long-read transcriptome data using a greedy, quality value-based algorithm
K Sahlin, P Medvedev - Journal of Computational Biology, 2020 - liebertpub.com
Long-read sequencing of transcripts with Pacific Biosciences (PacBio) Iso-Seq and Oxford
Nanopore Technologies has proven to be central to the study of complex isoform …
Nanopore Technologies has proven to be central to the study of complex isoform …
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm
K Sahlin, P Medvedev - … in Computational Molecular Biology: 23rd Annual …, 2019 - Springer
Long-read sequencing of transcripts with PacBio Iso-Seq and Oxford Nanopore
Technologies has proven to be central to the study of complex isoform landscapes in many …
Technologies has proven to be central to the study of complex isoform landscapes in many …
Using Mendelian inheritance to improve high-throughput SNP discovery
Restriction site-associated DNA sequencing or genotyping-by-sequencing (GBS)
approaches allow for rapid and cost-effective discovery and genotyping of thousands of …
approaches allow for rapid and cost-effective discovery and genotyping of thousands of …
Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments
The construction of genome-wide mutant collections has enabled high-throughput, high-
dimensional quantitative characterization of gene and chemical function, particularly via …
dimensional quantitative characterization of gene and chemical function, particularly via …
Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site
Y Monden, N Fujii, K Yamaguchi, K Ikeo… - …, 2014 - cdnsciencepub.com
Retrotransposons have been used frequently for the development of molecular markers by
using their insertion polymorphisms among cultivars, because multiple copies of these …
using their insertion polymorphisms among cultivars, because multiple copies of these …