BHSC_Bioinformatics/refs.html at master · deannachurch/BHSC_Bioinformatics · GitHub

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        <div id="header"><h1>Bar Harbor Short Course on Medical and Experimental Mammalian Genetics</h1></div>
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            <div id="sidebar"><h4>Pages</h4>
                <ul id="nav">
                    <li><a href="../index.html">Home</a></li>
                    <li><a href="../2014_07_21">Day 1</a></li>
                    <li><a href="../2014_07_23">Day 2</a></li>
                    <li><a href="../2014_07_24">Day 3</a></li>
                    <li><a href="../2014_07_25">Day 4</a></li>
                    <li><a href="../2014_07_29">Day 5</a></li>
                    <li><a href="refs.html">References</a></li>
                    <li><a href="formats.html">File Formats</a></li>
                    <li><a href="links.html">Resources</a></li>
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                <h2>Papers and references related to questions and topics discussed during the workshops</h2>
                <fieldset>
                <legend>File formats</legend>
                <p>The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.<a href="http://www.ncbi.nlm.nih.gov/pubmed/20015970">Cock et al., 2010</a></p>
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                <legend>Alignments</legend>
                <p>Basic local alignment search tool.<a href="http://www.ncbi.nlm.nih.gov/pubmed/2231712">Altschul SF, et al., 1990</a></p>
                <p>BLAT--the BLAST-like alignment tool.<a href="http://www.ncbi.nlm.nih.gov/pubmed/11932250">Kent WJ, 2002</a></p>
                <p>BLAST <a href="http://shop.oreilly.com/product/9780596002992.do">Korf et al., 2003</a>: Note: the book is a little dated with respect to some screen shots, but the background information is very useful.</p>
                <p>The Sequence Alignment/Map format and SAMtools. <a href="http://www.ncbi.nlm.nih.gov/pubmed/19505943" title="PubMed link">Li H et al., 2009</a></p>
                <p>Fast and accurate short read alignment with Burrows-Wheeler transform. <a href="http://www.ncbi.nlm.nih.gov/pubmed/19451168" title="PubMed link">Li H and Durbin R, 2009</a></p>
                <p>A survery of sequence alignment algorithms for next-generation sequencing. <a href="http://www.ncbi.nlm.nih.gov/pubmed/20460430" title="PubMed link">Li H and Homer N, 2010</a></p>
                <p>Tools for mapping high-throughput sequencing data. <a href="http://www.ncbi.nlm.nih.gov/pubmed/23060614" title="PubMed link">Fonseca N et al., 2012</a></p>
                <p>The variant call format and VCFtools. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21653522" title="PubMed link">Danacek P et al., 2012</a></p>
                <p>A standard variation file format for human genome sequences. <a href="http://www.ncbi.nlm.nih.gov/pubmed/20796305" title="PubMed link"> Reese MG et al., 2010</a></p>
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                <legend>Next Generation Sequencing</legend>
                <p>Bioinformatics collection: <a href="http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html">A collection of NGS papers published in Bioinformatics</a></p>
                <p>Challenges of sequencing human genomes. <a href="http://http//www.ncbi.nlm.nih.gov/pubmed/20519329" title="PubMed link">Koboldt et al., 2010</a></p>
                <p>A framework for variation discovery and genotyping using next-generation DNA sequencing data. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21478889" title="PubMed link">DePristo MA et al., 2011</a></p>
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            <legend>Genome Analysis</legend>
            <p>Diversity of human copy number variation and multicopy genes.<a href="http://http//www.ncbi.nlm.nih.gov/pubmed/21030649" title="PubMed link">Sudmant et al., 2010</a></p>
            <p>A map of human genome variation from population-scale sequencing. <a href="http://www.ncbi.nlm.nih.gov/pubmed/20981092" title="PubMed link">1000 Genomes Project Consortium</a></p>
            <p>A systematic survey of loss-of-function variants in human protein-coding genes. <a href="http://www.ncbi.nlm.nih.gov/pubmed/22344438" title="PubMed link">MacArthur DG et al., 2012</a></p>
            <p>Choice of transcripts and software has a large effect on variant annotation. <a href="http://www.ncbi.nlm.nih.gov/pubmed/24944579" title="PubMed link">McCarthy DJ et al., 2014</a></p>
            <p>A general framework for estimating the relative pathogenicity of human genetic variants. <a href="http://www.ncbi.nlm.nih.gov/pubmed/24487276" title="PubMed link">Kircher M et al., 2014</a></p>
            <p>Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. <a href="http://www.ncbi.nlm.nih.gov/pubmed/23537139" title="PubMed link">O'Rawe J et al., 2013</a></p>
            <p>Guidelines for investigating causality of sequence variants in human disease. <a href="http://www.ncbi.nlm.nih.gov/pubmed/24759409" title="PubMed link">MacArthur DG et al., 2014</a></p>
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