261 citations · 635 across the 5 of their papers we have counts for
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These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure
Qingpeng Zhang, Jason Pell, Rosangela Canino-Koning +2
K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing cover…
Assembling large, complex environmental metagenomes
Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti +3
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively re…
Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets
Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning +5
Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and i…
A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data
C. Titus Brown, Adina Howe, Qingpeng Zhang +2
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystem…
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
Jason Pell, Arend Hintze, Rosangela Canino-Koning +3
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotg…