http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.htmlA great list on free and paid softwares for nextgen sequence analysis is available at the seqanswers forum here.
To browse through a compiled list of Bioinformatics Softwares click here.
A list of publications devoted at the Bioinformatics journal here
Now I am working on samtools and bowtie and will write a detailed review soon...
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