Jose M. Abuin web page
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HPC
Big Data in metagenomics: Apache Spark vs MPI
The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in …
José M. Abuín
,
Nuno Lopes
,
Luís Ferreira
,
Tomás F. Pena
,
Bertil Schmidt
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DOI
VeryFastTree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies
Motivation: FastTree-2 is one of the most successful tools for inferring large phylogenies. With speed at the core of its design, there …
Cesar Piñeiro
,
José M. Abuín
,
Juan C. Pichel
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DOI
A Big Data Approach to Metagenomics for All-Food-Sequencing
Background: All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification …
Robin Kobus
,
José M. Abuín
,
André Müller
,
Sören Lukas Hellmann
,
Juan C. Pichel
,
Tomás F. Pena
,
Andreas Hildebrandt
,
Thomas Hankeln
,
Bertil Schmidt
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DOI
PASTASpark: multiple sequence alignment meets Big Data
Motivation: One basic step in many bioinformatics analyses is the Multiple Sequence Alignment (MSA). One of the state of the art tools …
José M. Abuín
,
Tomás F. Pena
,
Juan C. Pichel
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DOI
SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data
Next-generation sequencing (NGS) technologies have led to a huge amount of genomic data that need to be analyzed and interpreted. This …
José M. Abuín
,
Juan C. Pichel
,
Tomás F. Pena
,
Jorge Amigo
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DOI
BigBWA: Approaching the Burrows-Wheeler Aligner to Big Data Technologies
BigBWA is a new tool that uses the Big Data technology Hadoop to boost the performance of the Burrows-Wheeler Aligner (BWA). Important …
José M. Abuín
,
Juan C. Pichel
,
Tomás F. Pena
,
Jorge Amigo
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DOI
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