...-t INT : Number of threads (<= 100, default 1)...-f FILE1 [FILE2 ...]: Reads file (fasta or fastq format,...Map paired-end (mate-pair) reads on contigs, determine the ord...Map paired-end(mate-pair) reads on scaffolds, assemble reads...
Some useful links on Nanopore:
Decoding long nanopore sequencing reads of natural DNA:http://www.nature.com/nbt/journal/v32/n8/full/nbt.2950.html
Related links:- Data from pocket-sized genome sequencer unveiled http://www.nature.com/news/data-from-pocket-sized-genome-sequencer-unveiled-1.14724
Long reads are here to rule. Thanks to Nick Loman from Birmingham UK, now we can have our first look at long reads from Oxford Nanopore. http://nextgenseek.com/2014/06/behold-oxford-nanopore-reads-are-here/
TopHat http://tophat.cbcb.umd.edu/manual.shtml is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.