User:Jarle Pahr/Alignment

List of HTS mappers: http://wwwdev.ebi.ac.uk/fg/hts_mappers/

Software

Crossbow: http://bowtie-bio.sourceforge.net/crossbow/manual.shtml#what-is-crossbow

Bowtie: http://genomebiology.com/2009/10/3/r25

Genomer - A swiss army knife for Genome scaffolding:

Genomer tutorial: http://www.youtube.com/watch?v=HfsdJOELFjs

http://bioinf.wehi.edu.au/subread/

http://www.stormseq.org/

LAST: http://seqanswers.com/wiki/LAST

Information

http://www.homolog.us/blogs/blog/2013/08/06/mapping-algorithms-how-they-all-arrived/

http://genome.sph.umich.edu/wiki/Evaluating_a_Read_Mapper_on_Simulated_Data

http://biomickwatson.wordpress.com/2012/12/28/an-embargo-on-short-read-alignment-software/

Comparisons and reviews

http://bib.oxfordjournals.org/content/11/5/473.full

Tools for mapping high-throughput sequencing data: http://bioinformatics.oxfordjournals.org/content/28/24/3169