<commit_before>---
layout: page
title: Reading
tags: [papers,publications,ngs,background]
modified: 2014-08-08T20:53:07.573882-04:00
comments: false
image:
  feature: banner-papers.jpg
  credit: GalleryHip
  creditlink: http://galleryhip.com/pile-of-papers-on-desk.html
---

<section id="table-of-contents" class="toc">
  <header>
    <h3>Overview</h3>
  </header>
<div id="drawer" markdown="1">
*  Auto generated table of contents
{:toc}
</div>
</section><!-- /#table-of-contents -->

This page contains pointers to additional reading material and external resources relevant to the course. The page will be updated prior to every workshop and links and tips are very much welcome!

## General considerations

* Things to consider [when picking a sequencing facility](http://biomickwatson.wordpress.com/2013/01/21/ten-things-to-consider-when-choosing-an-ngs-supplier/)
* Excellent list of [introductory NGS papers](http://core-genomics.blogspot.com/2012/12/introductory-references-for-ngs-newbies.html?spref=tw)
* A more detailed list focusing on [all things RNA-Seq](http://www.ngswatch.com/rna-seq/) or [DNA-Seq](http://www.ngswatch.com/dna-seq-101/)
* Search portal for [NGS papers linked to disease, platform, mutations and Co](http://bioinfo.mc.vanderbilt.edu/NGS/index.html)

## Introduction

* [Organizing your data](..../documents/introduction/PLoS%20Comput%20Biol%202009%20Noble.pdf) (PDF)
* [Array reproducibilty](../documents/introduction/Nat%20Genet%202009%20Ioannidis.pdf) (PDF)
* [Keith Baggerly video lecture](http://videolectures.net/cancerbioinformatics2010_baggerly_irrh/)
* [<NAME> on better NGS experiments](http://core-genomics.blogspot.com/2012/10/how-to-do-better-ngs-experiments.html)

## QC and general sequence alignment

* [FASTQ format](../documents/QC/Nucleic%20Acids%20Res%202009%20Cock.pdf) (PDF)
* [k-mer analysis](../documents/QC/PLoS%20ONE%202010%20Schr%C3%B6der.pdf) (PDF)
* [ContEst](../documents/QC/Bioinformatics%202011%20Cibulskis.pdf) (PDF)
* [SeqTrim](../documents/QC/BMC%20Bioinformatics%202010%20Falgueras.pdf) (PDF)<commit_msg>Fixed more URLs in about and reading pages<commit_after>---
layout: page
title: Reading
tags: [papers,publications,ngs,background]
modified: 2014-08-08T20:53:07.573882-04:00
comments: false
image:
  feature: banner-papers.jpg
  credit: GalleryHip
  creditlink: http://galleryhip.com/pile-of-papers-on-desk.html
---

<section id="table-of-contents" class="toc">
  <header>
    <h3>Overview</h3>
  </header>
<div id="drawer" markdown="1">
*  Auto generated table of contents
{:toc}
</div>
</section><!-- /#table-of-contents -->

This page contains pointers to additional reading material and external resources relevant to the course. The page will be updated prior to every workshop and links and tips are very much welcome!

## General considerations

* Things to consider [when picking a sequencing facility](http://biomickwatson.wordpress.com/2013/01/21/ten-things-to-consider-when-choosing-an-ngs-supplier/)
* Excellent list of [introductory NGS papers](http://core-genomics.blogspot.com/2012/12/introductory-references-for-ngs-newbies.html?spref=tw)
* A more detailed list focusing on [all things RNA-Seq](http://www.ngswatch.com/rna-seq/) or [DNA-Seq](http://www.ngswatch.com/dna-seq-101/)
* Search portal for [NGS papers linked to disease, platform, mutations and Co](http://bioinfo.mc.vanderbilt.edu/NGS/index.html)

## Introduction

* [Organizing your data](../documents/introduction/PLoS%20Comput%20Biol%202009%20Noble.pdf) (PDF)
* [Array reproducibilty](../documents/introduction/Nat%20Genet%202009%20Ioannidis.pdf) (PDF)
* [<NAME> video lecture](http://videolectures.net/cancerbioinformatics2010_baggerly_irrh/)
* [<NAME> on better NGS experiments](http://core-genomics.blogspot.com/2012/10/how-to-do-better-ngs-experiments.html)

## QC and general sequence alignment

* [FASTQ format](../documents/QC/Nucleic%20Acids%20Res%202009%20Cock.pdf) (PDF)
* [k-mer analysis](../documents/QC/PLoS%20ONE%202010%20Schr%C3%B6der.pdf) (PDF)
* [ContEst](../documents/QC/Bioinformatics%202011%20Cibulskis.pdf) (PDF)
* [SeqTrim](../documents/QC/BMC%20Bioinformatics%202010%20Falgueras.pdf) (PDF)
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