NextGen genomics guide
Reference Articles:
- Next-generation DNA sequencing
Jay Shendure & Hanlee Ji
- Exome sequencing as a tool for Mendelian disease gene discovery
Michael J. Bamshad, Sarah B. Ng, Abigail W. Bigham, Holly K. Tabor, Mary J. Emond, Deborah A. Nickerson & Jay Shendure
- A beginners guide to SNP calling from high-throughput DNA-sequencing data
Andre´ Altmann, Peter Weber, Daniel Bader, Michael Preuss, Elisabeth B. Binder & Bertram Mu¨ller-Myhsok
- Transcriptome analysis using next-generation sequencing
Kai-Oliver Mutz, Alexandra Heilkenbrinker, Maren Lönne, Johanna-Gabriela Walter & Frank Stahl
- Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era
Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun & Hana Yi
- QIIME allows analysis of high-throughput community sequencing data
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld & Rob Knight
NextGen Tools:
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead, Cole Trapnell, Mihai Pop & Steven L Salzberg
- Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li & Richard Durbin
- The Sequence Alignment/Map format and SAMtools
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Home, Gabor Marth, Goncalo Abecasis, Richard Durbin & 1000 Genome Project Data Processing Subgroup
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Helga Thorvaldsdóttir, James T. Robinson & Jill P. Mesirov
- TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell, Lior Pachter & Steven L. Salzberg