From 4ca645222f2e4305b13f34ee80fe030ddb941c65 Mon Sep 17 00:00:00 2001 From: Leszek Pryszcz Date: Thu, 10 Mar 2016 15:08:16 +0100 Subject: [PATCH] docs --- README.md | 2 +- docs/README.md | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 3374151..beea39c 100644 --- a/README.md +++ b/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) diff --git a/docs/README.md b/docs/README.md index 568ff06..96c438f 100644 --- a/docs/README.md +++ b/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.