Biology subjects

Steven L Salzberg

Publications and source records attributed to Steven L Salzberg.

3 recordsLinked to original sources

bioRxiv2016

Centrifuge: rapid and sensitive classification of metagenomic sequences

Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4,078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI non-redundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer based indexing schemes, which require far more extensive space. Centrifuge is available as free, open-source software from www.ccb.jhu.edu/software/centrifuge

Bioinformatics↗

bioRxiv2016

Bracken: Estimating species abundance in metagenomics data

We describe a new, highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is shared with other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species-and genus-level abundance estimates even when a sample contains multiple near-identical species.

Bioinformatics↗

bioRxiv2014

Flexible analysis of transcriptome assemblies with Ballgown

Introduction Introduction Negative control experiment Positive control experiment Confirmation of statistical... Analysis of RNA-seq experiments... Analysis of quantitative... Expression quantitative trait... Computational Efficiency Summary References A key advantage of RNA sequencing (RNA-seq) over hybridization-based technologies such as microarrays is that RNA-seq makes it possible to reconstruct complete gene structures, including multiple splice variants, from raw RNA-seq reads without relying on previously-established annotations [20, 32, 9]. But with this added flexibility, there are increased computational demands on upstream processing tasks such as alignment and ass ...

Bioinformatics↗