Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

By Paolo Di Tommaso, Miquel Orobitg, F. Guirado, F. Cores, Toni Espinosa, Cédric Notredame. Bioinform., 2010

676 citations recorded by the source corpus.

Summary: We present the first parallel implementation of the T-Coffee consistency-based multiple aligner. We benchmark it on the Amazon Elastic Cloud (EC2) and show that the parallelization procedure is reasonably effective. We also conclude that for a web server with moderate usage (10K hits/month) the cloud provides a cost-effective alternative to in-house deployment. Availability: T-Coffee is a freeware open source package available from http://www.tcoffee.org/homepage.html Contact: cedric.notredame@crg.es

Subfields: Artificial Intelligence, Computer Networks and Communications, Information Systems and Management

View Paper: https://www.semanticscholar.org/paper/647614399939bddabe88ef47e0b6dda45d5b3326

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Citations in the corpus

Accurate, scalable and integrative haplotype estimation (2019, methodology): “All the input and output interface implemented in SHAPEIT4 is built on the High-Throughput Sequencing library (HTSlib 30,31 ) so that genotype and haplotype data is read and written in either variant call format (VCF) or its binary version; the BCF format.”
vcfr: a package to manipulate and visualize variant call format data in R (2017, methodology): “A VCF file consists of a text file structured according to the VCF specification (Danecek et al. 2011; Samtools 2016).”
The UCSC Genome Browser database: 2014 update (2013, methodology): “Track hubs now support four compressed binary indexed ﬁle formats: BigBed and BigWig (27), both developed at UCSC, BAM (28) and VCF/tabix (29).”
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation (2017, methodology): “Inspired by models and algorithms developed for detecting contamination in DNA sequencing 18 , demuxlet is fast, accurate, scalable, and compatible with standard input formats 17, 19, 20 .”
Dsuite - fast D-statistics and related admixture evidence from VCF files (2020, methodology): “Dsuite has a user-friendly straightforward workflow and uses the standard VCF format, thus generally avoiding the need for format conversions or data duplication.”
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments (2016, methodology): “The VCF output retains the position of the SNPs in each sample and can be parsed using standard tools such as BCFtools (Danecek et al., 2011) or for GWAS analysis using PLINK (Chang et al., 2015).”
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants (2011, methodology): “VCFTools (33) was used to perform the calculation, using an LD threshold of r 2 = 0.80, and a maximum distance between variants of 200 kb. Results from VCFTools were then consolidated such that for every variant in our database, a list of linked variants is accessible for each of the three…”