Velvet Hands-on Exercise

General information
The following standard icons are used in the hands-on exercises to help to locate
Important Information

General information / notes

Follow the following steps

Questions to be answered

Warning – PLEASE take care and read carefully

Optional Bonus exercise

Optional Bonus exercise for a champion

Resources used
velvet http://www.ebi.ac.uk/~zerbino/velvet/
velvet user email list http://listserver.ebi.ac.uk/mailman/listinfo/velvet-users
velvet Columbus manual http://www.ebi.ac.uk/~zerbino/velvet/Columbus_manual.pdf
velvet Oases http://www.ebi.ac.uk/~zerbino/oases/
Oases user email list http://listserver.ebi.ac.uk/mailman/listinfo/oases-users
MetaVelvet http://metavelvet.dna.bio.keio.ac.jp/

R http://www.r-project.org/
tablet http://bioinf.scri.ac.uk/tablet/
fastqc http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
fastqc youtube tutorial http://www.youtube.com/watch?v=bz93ReOv87Y
trimFastqReads.pl http://curtain.googlecode.com/hg/curtain-exec/src/main/bin/trimFastqReads.pl
Trim.pl http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.pl
gnx https://github.com/mh11/gnx-tools

Further useful tools

samtools http://samtools.sourceforge.net/
bwa http://bio-bwa.sourceforge.net/
jellyfish http://www.cbcb.umd.edu/software/jellyfish/
quake http://www.cbcb.umd.edu/software/quake/

Further reading
Velvet Paper http://genome.cshlp.org/content/18/5/821.short
Velvet Pebble & Rock Band http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008407
Assemblathon 1 http://genome.cshlp.org/content/21/12/2224.abstract
Velvet protocol http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1105s31/abstract
Oases http://bioinformatics.oxfordjournals.org/content/early/2012/02/24/bioinformatics.bts094.abstract

09/03/12 1/1 MH/DJ