754 citations · 1.5k across the 9 of their papers we have counts for
9 papers
Sustainable computational science: the ReScience initiative
Nicolas P. Rougier, Konrad Hinsen, Frédéric Alexandre +42
Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In…
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…
RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates
Alexis Black Pyrkosz, Hans Cheng, C. Titus Brown
Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate d…
khmer: Working with Big Data in Bioinformatics
Eric McDonald, C. Titus Brown
We introduce design and optimization considerations for the 'khmer' package.
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…