Searching for SNPs with cloud computing

By Ben Langmead, Michael C. Schatz, Jimmy Lin, Mihai Pop, Steven L. Salzberg. Genome Biology, 2009

523 citations recorded by the source corpus.

As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/42fee5b7c0d96f93172ac64bfef5a888874f3ab6

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Citations in the corpus

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility (2012, background): “…open-source software packages that can scale well on cloud resources, but these are typically single-purpose (such as Crossbow for variant discovery 25 , Myrna for RNA-seq analyses 26 and CloVR for metagenomic and small-genome annotation projects 27 ) and thus may not be easily integrated into…”
A survey of sequence alignment algorithms for next-generation sequencing (2010, background): “Several researchers [26, 68] have explored this approach, but establishing a cloud computing framework requires the efforts of the entire community.”
A framework for variation discovery and genotyping using next-generation DNA sequencing data (2011, methodology): “Although the value of the data processing and error modeling presented here is also clear, applying local realignment and base quality score recalibration -- publicly available, easy-to-use modules in the GATK -- are likely to improve the results of the Crossbow pipeline.”
c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells (2012, unknown): “Sequence reads of 25 bp for ChIP-Seq and 36 bp for RNA-Seq were generated from an Illumina Genome Analyzer, mapped to mouse genome (mm8) by using Bowtie (Langmead et al., 2009).”
Big Data: Astronomical or Genomical? (2015, unknown): “Variant calling on 2 billion genomes per year, with 100,000 CPUs in parallel, would require methods that process 2 genomes per CPU-hour, three-to-four orders of magnitude faster than current capabilities [42].”
Cloud-scale RNA-sequencing differential expression analysis with Myrna (2010, background): “Recent studies and commentaries [13-17] propose cloud computing as a paradigm that counteracts this disparity by tapping into the economies of scale afforded by commercial and institutional computing centers.”
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads (2012, methodology): “In this process, read pairs are first aligned to reference sequences using short read alignment tools such as Bowtie [15], Crossbow [16], and BWA [17], and those read pairs that are exactly mapped to the same position are considered duplicate candidates.”
The impact of next-generation sequencing on genomics (2011, background): “CrossBow is the first cloud computing software capable of performing alignment and single nucleotide polymorphism analysis on multiple whole-human datasets (Langmead et al., 2009).”
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics (2010, methodology): “Following release of Cloudburst, Schatz and colleagues at UMD and at Johns Hopkins University (e.g., B. Lang-mead) have developed a suite of algorithms that employ Hadoop for analysis of next generation sequencing data: 1) Crossbow [43,44] uses Hadoop for its calculations for whole genome resequenci”
Computational solutions to large-scale data management and analysis (2010, background): “and aligning raw sequencing reads to reference genome”
'Big data', Hadoop and cloud computing in genomics (2013, methodology): “analysis Crossbow A scalable software pipeline that combines Bowtie and SoapSNP for whole genome re-sequencing analysis [46]”