docs

Author: Leszek Pryszcz

README.md

@@ -29,7 +29,7 @@ so it can be run even on the laptop for small-to-medium size genomes
 - **flexible** toward many sequencing technologies (Illumina, 454 or Sanger) and library types (paired-end, mate pairs, fosmids)
 - **modular**: every step can be ommited or replaced by another tools
 
-For more information have a look at the [poster](/docs/poster.pdf) or [manuscript](/docs/manuscript.pdf).
+For more information have a look at the [documentation](/docs), [poster](/docs/poster.pdf) or [manuscript](/docs/manuscript.pdf).
 
 ![Flowchart](/docs/redundans_flowchart.png)
 

docs/README.md

@@ -2,7 +2,6 @@
 - **[Redundans docs](#redundans-docs)**  
   - **[FAQ](#faq)**
   - **[FAQ - INSTALL.sh](#faq---installsh)**
-  - **[Citation](#citation)**
 
 # Redundans docs
 
@@ -56,7 +55,7 @@ IOError: [Errno 2] No such file or directory: '.../test/run11/_sspace.1.1.fa'
 ### Why does Redundans use two similarity search algorithms, [BLAT](https://genome.ucsc.edu/FAQ/FAQblat.html#blat3) & [LAST](http://last.cbrc.jp/)?   
 BLAT is lightweight & very fast, but lack sensitivity for more diverged sequences. If you specify `--identity` below 0.85, the pipeline will use LAST, that is ~4x slower, but more sensitive than BLAT.
 Our simulations shows LAST is capable of correctly reducing heterozygous assemblies with up to 45% divergence between haplotypes.   
-To limit speed difference between these two algorithms, LAST **runs in multiple threads**, so using `-t 4` you shouldn't see any difference in runtime between runs for `--identity 0.9` or `--identity 0.5`. Note, this only works in Python 2.7! 
+To limit speed difference between these two algorithms, LAST **runs in multiple threads**, so using `-t 4` you shouldn't see any difference in runtime between runs for `--identity 0.9` or `--identity 0.5`. 
 
 ### How is multiple redundancy handled? 
 Redundans removes all contigs, but the longest one, that fullfill identity & overlap critaria during reduction step. For more info see [issue #8](https://github.com/lpryszcz/redundans/issues/8).
@@ -65,6 +64,9 @@ Redundans removes all contigs, but the longest one, that fullfill identity & ove
 https://github.com/Gabaldonlab/redundans is the official repository for Redundans, but we keep https://github.com/lpryszcz/redundans for back-compatibility, as some of the very first users of Redundans use it.
 **Both Redundans repositories contain the same code and are regularly updated.**
 
+### How to cite Redundans?
+Leszek P. Pryszcz and Toni Gabaldón (Submitted) Redundans: an assembly pipeline for highly heterozygous genomes. NAR
+
 ## FAQ - INSTALL.sh
 ### Installation succeeded, but redundans fails with `ImportError: No module named Bio`
 Make sure you opened new terminal window after installation finished.