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Another small README typo
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mstubb committed Oct 14, 2015
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Expand Up @@ -26,7 +26,7 @@ Tracer relies on several additional tools and Python modules that you should ins

####Software####
1. [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) - required for alignment of reads to synthetic TCR genomes.
2. [Trinity](http://sourceforge.net/projects/trinityrnaseq/files/PREV_CONTENTS/previous_releases/) - required for assembly of reads into TCR contigs. **Currently TraCeR uses Trinity parameters intended for use with [Trinity v1.0](http://sourceforge.net/projects/trinityrnaseq/files/PREV_CONTENTS/previous_releases/). Updates for use with [Trinity v2.0](https://github.com/trinityrnaseq/trinityrnaseq/wiki) are coming soon.**
2. [Trinity](http://sourceforge.net/projects/trinityrnaseq/files/PREV_CONTENTS/previous_releases/) - required for assembly of reads into TCR contigs. **Currently TraCeR uses Trinity parameters intended for use with [Trinity v1](http://sourceforge.net/projects/trinityrnaseq/files/PREV_CONTENTS/previous_releases/). Updates for use with [Trinity v2](https://github.com/trinityrnaseq/trinityrnaseq/wiki) are coming soon.**
3. [IgBLAST](http://www.ncbi.nlm.nih.gov/igblast/faq.html#standalone) - required for analysis of assembled contigs. [FTP site](ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/).
4. [Kallisto](http://pachterlab.github.io/kallisto/) - required for quantification of TCR expression.
5. [Graphviz](http://www.graphviz.org) - Dot and Neato drawing programs required for visualisation of clonotype graphs.
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