�ݺ�ߣshows by User: lucacozzuto

�ݺ�ߣshows by User: lucacozzuto / http://www.slideshare.net/images/logo.gif �ݺ�ߣshows by User: lucacozzuto / Mon, 15 Apr 2019 15:08:37 GMT �ݺ�ߣShare feed for �ݺ�ߣshows by User: lucacozzuto vectorQC: 'A pipeline for assembling and annotation of vectors' /slideshow/vectorqc-a-pipeline-for-assembling-and-annotation-of-vectors/140885123 cozzutocompdataseminar2019-190415150837
DNA vectors are widely used in molecular cloning, gene engineering, studies of gene expression and other applications. Sequence validation of a vector DNA is a crucial quality control step before using the vector. With the cost of sequencing rapidly decreasing it becomes cost-effective to ensure the vectors quality using high-throughput sequencing and bioinformatics analysis. VectorQC is an automatic pipeline for quality control of a collection of sequenced DNA vectors. The pipeline is built using the NextFlow framework and is distributed with the Docker container, which makes the pipeline easy to install, modify, and re-use on any Unix-compatible OS on a computer, cluster or cloud]]>
DNA vectors are widely used in molecular cloning, gene engineering, studies of gene expression and other applications. Sequence validation of a vector DNA is a crucial quality control step before using the vector. With the cost of sequencing rapidly decreasing it becomes cost-effective to ensure the vectors quality using high-throughput sequencing and bioinformatics analysis. VectorQC is an automatic pipeline for quality control of a collection of sequenced DNA vectors. The pipeline is built using the NextFlow framework and is distributed with the Docker container, which makes the pipeline easy to install, modify, and re-use on any Unix-compatible OS on a computer, cluster or cloud]]> Mon, 15 Apr 2019 15:08:37 GMT /slideshow/vectorqc-a-pipeline-for-assembling-and-annotation-of-vectors/140885123 lucacozzuto@slideshare.net(lucacozzuto) vectorQC: 'A pipeline for assembling and annotation of vectors' lucacozzuto DNA vectors are widely used in molecular cloning, gene engineering, studies of gene expression and other applications. Sequence validation of a vector DNA is a crucial quality control step before using the vector. With the cost of sequencing rapidly decreasing it becomes cost-effective to ensure the vectors quality using high-throughput sequencing and bioinformatics analysis. VectorQC is an automatic pipeline for quality control of a collection of sequenced DNA vectors. The pipeline is built using the NextFlow framework and is distributed with the Docker container, which makes the pipeline easy to install, modify, and re-use on any Unix-compatible OS on a computer, cluster or cloud <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/cozzutocompdataseminar2019-190415150837-thumbnail.jpg?width=120&height=120&fit=bounds" /> DNA vectors are widely used in molecular cloning, gene engineering, studies of gene expression and other applications. Sequence validation of a vector DNA is a crucial quality control step before using the vector. With the cost of sequencing rapidly decreasing it becomes cost-effective to ensure the vectors quality using high-throughput sequencing and bioinformatics analysis. VectorQC is an automatic pipeline for quality control of a collection of sequenced DNA vectors. The pipeline is built using the NextFlow framework and is distributed with the Docker container, which makes the pipeline easy to install, modify, and re-use on any Unix-compatible OS on a computer, cluster or cloud

vectorQC: 'A pipeline for assembling and annotation of vectors' from Luca Cozzuto

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0 Course on parsing methods for biologists with a focus on ChIP-seq data /lucacozzuto/course-on-parsing-methods-for-biologists-with-a-focus-on-chipseq-data phdcourse-181024122003
This presentation is about data formats in bioinformatics and basic linux tools. The focus is on Chip-Seq experiment. ]]>
This presentation is about data formats in bioinformatics and basic linux tools. The focus is on Chip-Seq experiment. ]]> Wed, 24 Oct 2018 12:20:03 GMT /lucacozzuto/course-on-parsing-methods-for-biologists-with-a-focus-on-chipseq-data lucacozzuto@slideshare.net(lucacozzuto) Course on parsing methods for biologists with a focus on ChIP-seq data lucacozzuto This presentation is about data formats in bioinformatics and basic linux tools. The focus is on Chip-Seq experiment. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/phdcourse-181024122003-thumbnail.jpg?width=120&height=120&fit=bounds" /> This presentation is about data formats in bioinformatics and basic linux tools. The focus is on Chip-Seq experiment.

Course on parsing methods for biologists with a focus on ChIP-seq data from Luca Cozzuto

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0 From Zero to Nextflow 2017 /slideshow/from-zero-to-nextflow-2017/79809028 cozzutonextflow-170915131502
The Bioinformatics Core Facility implemented during the years a number of procedures and pipelines for providing high quality results to an increasing number of users. Here we present our experience with migrating some of extensively used pipelines to the Nextflow framework and creating docker/singularity containers for reproducibility.]]>
The Bioinformatics Core Facility implemented during the years a number of procedures and pipelines for providing high quality results to an increasing number of users. Here we present our experience with migrating some of extensively used pipelines to the Nextflow framework and creating docker/singularity containers for reproducibility.]]> Fri, 15 Sep 2017 13:15:02 GMT /slideshow/from-zero-to-nextflow-2017/79809028 lucacozzuto@slideshare.net(lucacozzuto) From Zero to Nextflow 2017 lucacozzuto The Bioinformatics Core Facility implemented during the years a number of procedures and pipelines for providing high quality results to an increasing number of users. Here we present our experience with migrating some of extensively used pipelines to the Nextflow framework and creating docker/singularity containers for reproducibility. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/cozzutonextflow-170915131502-thumbnail.jpg?width=120&height=120&fit=bounds" /> The Bioinformatics Core Facility implemented during the years a number of procedures and pipelines for providing high quality results to an increasing number of users. Here we present our experience with migrating some of extensively used pipelines to the Nextflow framework and creating docker/singularity containers for reproducibility.

From Zero to Nextflow 2017 from Luca Cozzuto

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0 Benchmarking 16S rRNA gene sequencing and bioinformatics tools for identification of microbial abundances /slideshow/benchmarking-16s-rrna-gene-sequencing-and-bioinformatics-tools-for-identification-of-microbial-abundances/60814652 2016-04-ngs2016-posterfinal-160412143451
High-throughput DNA sequencing continue to offer comprehensive insights into microbial ecosystems1. Several bioinformatics tools have been inconclusively benchmarked2, yet variations in algorithms are known to impact the microbiome results3. Thus, there is need for detailed benchmarking of bioinformatics tools. Here we validated 16S rRNA amplicon sequencing and four bioinformatics tools for microbiome analyses.]]>
High-throughput DNA sequencing continue to offer comprehensive insights into microbial ecosystems1. Several bioinformatics tools have been inconclusively benchmarked2, yet variations in algorithms are known to impact the microbiome results3. Thus, there is need for detailed benchmarking of bioinformatics tools. Here we validated 16S rRNA amplicon sequencing and four bioinformatics tools for microbiome analyses.]]> Tue, 12 Apr 2016 14:34:51 GMT /slideshow/benchmarking-16s-rrna-gene-sequencing-and-bioinformatics-tools-for-identification-of-microbial-abundances/60814652 lucacozzuto@slideshare.net(lucacozzuto) Benchmarking 16S rRNA gene sequencing and bioinformatics tools for identification of microbial abundances lucacozzuto High-throughput DNA sequencing continue to offer comprehensive insights into microbial ecosystems1. Several bioinformatics tools have been inconclusively benchmarked2, yet variations in algorithms are known to impact the microbiome results3. Thus, there is need for detailed benchmarking of bioinformatics tools. Here we validated 16S rRNA amplicon sequencing and four bioinformatics tools for microbiome analyses. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/2016-04-ngs2016-posterfinal-160412143451-thumbnail.jpg?width=120&height=120&fit=bounds" /> High-throughput DNA sequencing continue to offer comprehensive insights into microbial ecosystems1. Several bioinformatics tools have been inconclusively benchmarked2, yet variations in algorithms are known to impact the microbiome results3. Thus, there is need for detailed benchmarking of bioinformatics tools. Here we validated 16S rRNA amplicon sequencing and four bioinformatics tools for microbiome analyses.

Benchmarking 16S rRNA gene sequencing and bioinformatics tools for identification of microbial abundances from Luca Cozzuto

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0 AnnoWiki /slideshow/annowiki/35515037 2014-06-ngs2014-poster-v5-140605030218-phpapp02
Poster presented at Next Generation Sequencing Conference (NGS) 2014 held in Barcelona. http://www.iscb.org/ngs2014 ]]>
Poster presented at Next Generation Sequencing Conference (NGS) 2014 held in Barcelona. http://www.iscb.org/ngs2014 ]]> Thu, 05 Jun 2014 03:02:18 GMT /slideshow/annowiki/35515037 lucacozzuto@slideshare.net(lucacozzuto) AnnoWiki lucacozzuto Poster presented at Next Generation Sequencing Conference (NGS) 2014 held in Barcelona. http://www.iscb.org/ngs2014 <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/2014-06-ngs2014-poster-v5-140605030218-phpapp02-thumbnail.jpg?width=120&height=120&fit=bounds" /> Poster presented at Next Generation Sequencing Conference (NGS) 2014 held in Barcelona. http://www.iscb.org/ngs2014

AnnoWiki from Luca Cozzuto

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0 Macs course /lucacozzuto/macs-course macscourse-120420084526-phpapp01
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]]> Fri, 20 Apr 2012 08:45:25 GMT /lucacozzuto/macs-course lucacozzuto@slideshare.net(lucacozzuto) Macs course lucacozzuto <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/macscourse-120420084526-phpapp01-thumbnail.jpg?width=120&height=120&fit=bounds" />

Macs course from Luca Cozzuto

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0 Annotating nc-RNAs with Rfam /lucacozzuto/annotating-ncrnas-with-rfam rfam-101221033005-phpapp02
Rfam is an open access database (hosted at the Wellcome Trust Sanger Institute) containing information for RNA families and annotations for millions of RNA genes. Designed to work in a similar way to the Pfam database of protein families, Rfam uses a similar model for annotation and display and is built on the same principle of open access to the data. Each entry in the Rfam database includes multiple sequence alignments, a secondary structure and probabilistic models known as covariance models (CMs), these models can simultaneously handle an RNA sequence and its structure. In conjunction with the Infernal software package, Rfam CMs can be used to search genomes or other DNA sequence databases for homologs to known structural RNA families. You can find more about Rfam at http://rfam.janelia.org/]]>
Rfam is an open access database (hosted at the Wellcome Trust Sanger Institute) containing information for RNA families and annotations for millions of RNA genes. Designed to work in a similar way to the Pfam database of protein families, Rfam uses a similar model for annotation and display and is built on the same principle of open access to the data. Each entry in the Rfam database includes multiple sequence alignments, a secondary structure and probabilistic models known as covariance models (CMs), these models can simultaneously handle an RNA sequence and its structure. In conjunction with the Infernal software package, Rfam CMs can be used to search genomes or other DNA sequence databases for homologs to known structural RNA families. You can find more about Rfam at http://rfam.janelia.org/]]> Tue, 21 Dec 2010 03:30:00 GMT /lucacozzuto/annotating-ncrnas-with-rfam lucacozzuto@slideshare.net(lucacozzuto) Annotating nc-RNAs with Rfam lucacozzuto Rfam is an open access database (hosted at the Wellcome Trust Sanger Institute) containing information for RNA families and annotations for millions of RNA genes. Designed to work in a similar way to the Pfam database of protein families, Rfam uses a similar model for annotation and display and is built on the same principle of open access to the data. Each entry in the Rfam database includes multiple sequence alignments, a secondary structure and probabilistic models known as covariance models (CMs), these models can simultaneously handle an RNA sequence and its structure. In conjunction with the Infernal software package, Rfam CMs can be used to search genomes or other DNA sequence databases for homologs to known structural RNA families. You can find more about Rfam at http://rfam.janelia.org/ <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/rfam-101221033005-phpapp02-thumbnail.jpg?width=120&height=120&fit=bounds" /> Rfam is an open access database (hosted at the Wellcome Trust Sanger Institute) containing information for RNA families and annotations for millions of RNA genes. Designed to work in a similar way to the Pfam database of protein families, Rfam uses a similar model for annotation and display and is built on the same principle of open access to the data. Each entry in the Rfam database includes multiple sequence alignments, a secondary structure and probabilistic models known as covariance models (CMs), these models can simultaneously handle an RNA sequence and its structure. In conjunction with the Infernal software package, Rfam CMs can be used to search genomes or other DNA sequence databases for homologs to known structural RNA families. You can find more about Rfam at http://rfam.janelia.org/

Annotating nc-RNAs with Rfam from Luca Cozzuto

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0 https://cdn.slidesharecdn.com/profile-photo-lucacozzuto-48x48.jpg?cb=1645457771 Bioinformatician expert of Next Generation Sequencing data analysis (PhD). Currently working at Centre for Genomic Regulation in Barcelona, Spain, as NGS data analysis coordinator in the Bioinformatics Core Facility. My work includes to supervise projects about a broad variety of NGS application such as assembly and annotation of genomic and transcriptomic data (mRNAseq and microRNAseq), detection of interaction protein/DNA and protein/RNA (chip-seq and clip-seq), metagenomic analysis. I'm also involved in pathway analysis, gene-set enrichment and motif detection. I participated in more than 60 different projects and in 3 international genome projects (melon, bean and lynx) being part of ... http://biocore.crg.cat/wiki/User:Lcozzuto https://cdn.slidesharecdn.com/ss_thumbnails/cozzutocompdataseminar2019-190415150837-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/vectorqc-a-pipeline-for-assembling-and-annotation-of-vectors/140885123 vectorQC: 'A pipeline ... https://cdn.slidesharecdn.com/ss_thumbnails/phdcourse-181024122003-thumbnail.jpg?width=320&height=320&fit=bounds lucacozzuto/course-on-parsing-methods-for-biologists-with-a-focus-on-chipseq-data Course on parsing meth... https://cdn.slidesharecdn.com/ss_thumbnails/cozzutonextflow-170915131502-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/from-zero-to-nextflow-2017/79809028 From Zero to Nextflow ...