Update and add citations

[greatfireball]

As discussed on our slack channel, we should add some more citations:

• [x] Jellyfish
• [x] Spades
• [x] bowtie2
• [x] NCBI-Blast+
• [x] Samtools
• [x] Bedtools
• [x] GNU R
• [x] Ghostscript
• [x] Python
• [x] Perl
• [x] diverse perl modules

[greatfireball]

@PfaffS added bowtie2, NCBI-Blast+, Samtools, Bedtools, and GNU R in paper.bib

[greatfireball]

@PfaffS please add links to the italic items to paper.md as inline links

[PfaffS]

added Ghostscript, Phyton, Perl and Perl moduls as inline links in paper.md

[greatfireball]

thx! Will you prepare a pull request and request review by @iimog or myself?

[PfaffS]

done, requested a pull. Review by @greatfireball and @iimog

[greatfireball]

:+1:

[greatfireball]

thx