[ci skip] start readme cleanup

README.md

@@ -1,31 +1,13 @@
 <img alt="salmon logo" src="https://github.com/COMBINE-lab/salmon/raw/master/doc/salmon_logo.png" width="600">
 
-[![Build Status](https://travis-ci.org/COMBINE-lab/salmon.svg?branch=master)](https://travis-ci.org/COMBINE-lab/salmon)
 [![Documentation Status](https://readthedocs.org/projects/salmon/badge/?version=latest)](http://salmon.readthedocs.org/en/latest)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/salmon/README.html)
 
 
-**Try out alevin (salmon's single-cell processing module)!  Get started with the [tutorial](https://combine-lab.github.io/alevin-tutorial/#blog)**
-
-**Try out the new [alevin-fry](https://alevin-fry.readthedocs.io/en/latest/) framework for single-cell analysis!**
+**Try out the new [alevin-fry](https://alevin-fry.readthedocs.io/en/latest/) framework for single-cell analysis; tutorials can be found [here](https://combine-lab.github.io/alevin-fry-tutorials/)!**
 
 **Help guide the development of Salmon, [take our survey](https://docs.google.com/forms/d/e/1FAIpQLSeWhBNE_fA_0uVHvbAlAulDmfmowv7rAYla879DZpqCARyRTQ/viewform)**
 
-### Pre-computed decoy transcriptomes 
-
-tl;dr: fast is good but fast and accurate is better !
-Although the precomputed decoys (<=v.14.2) are still compatible with the latest major release (v1.0.0). We recommend updating your index using the full genome, as it can give significantly higher accuracy. For more information, please check our extensive benchmarking comparing different alignment methods and their performance on RNA-seq quantification in the latest revised preprint [manuscript](https://www.biorxiv.org/content/10.1101/657874v2).
-Please use the [tutorial](https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/) for a step-by-step guide on how to efficiently index the reference transcriptome and genome for accurate gentrome based RNA-seq quantification.
-
-Specifically, there are 3 possible ways in which the salmon index can be created:
-
-* cDNA-only index : salmon_index - https://combine-lab.github.io/salmon/getting_started/. This method will result in the smallest index and require the least resources to build, but will be the most prone to possible spurious alignments.
-
-* SA mashmap index: salmon_partial_sa_index - (regions of genome that have high sequence similarity to the transcriptome) - Details can be found in [this README](https://github.com/COMBINE-lab/SalmonTools/blob/master/README.md) and using [this script](https://raw.githubusercontent.com/COMBINE-lab/SalmonTools/master/scripts/generateDecoyTranscriptome.sh). While running mashmap can require considerable resources, the resulting decoy files are fairly small.  This will result in an index bigger than the cDNA-only index, but still mucch smaller than the full genome index below.  It will confer many, though not all, of the benefits of using the entire genome as a decoy sequence.
-
-* SAF genome index: salmon_sa_index - (the full genome is used as decoy) - The tutorial for creating such an index can be found [here](https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/).  This will result in the largest index, but likely does the best job in avoiding spurious alignments to annotated transcripts. 
-
-**Facing problems with Indexing ?, Check if anyone else already had this problem in the issues section or fill the index generation [request form](https://forms.gle/3baJc5SYrkSWb1z48)**
 
 What is Salmon?
 ===============
@@ -48,9 +30,25 @@ The documentation for Salmon is available on [ReadTheDocs](http://readthedocs.or
 Salmon is, and will continue to be, [freely and actively supported on a best-effort basis](https://oceangenomics.com/about/#open).
 If you need industrial-grade technical support, please consider the options at [oceangenomics.com/contact](http://oceangenomics.com/contact).
 
+### Pre-computed decoy transcriptomes 
+
+tl;dr: fast is good but fast and accurate is better!
+Although the precomputed decoys (<=v.14.2) are still compatible with the latest major release (v1.5.1). We recommend updating your index using the full genome, as it can give significantly higher accuracy. For more information, please check our extensive benchmarking comparing different alignment methods and their performance on RNA-seq quantification in the latest revised preprint [manuscript](https://www.biorxiv.org/content/10.1101/657874v2).
+Please use the [tutorial](https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/) for a step-by-step guide on how to efficiently index the reference transcriptome and genome for accurate gentrome based RNA-seq quantification.
+
+Specifically, there are 3 possible ways in which the salmon index can be created:
+
+* cDNA-only index : salmon_index - https://combine-lab.github.io/salmon/getting_started/. This method will result in the smallest index and require the least resources to build, but will be the most prone to possible spurious alignments.
+
+* SA mashmap index: salmon_partial_sa_index - (regions of genome that have high sequence similarity to the transcriptome) - Details can be found in [this README](https://github.com/COMBINE-lab/SalmonTools/blob/master/README.md) and using [this script](https://raw.githubusercontent.com/COMBINE-lab/SalmonTools/master/scripts/generateDecoyTranscriptome.sh). While running mashmap can require considerable resources, the resulting decoy files are fairly small.  This will result in an index bigger than the cDNA-only index, but still mucch smaller than the full genome index below.  It will confer many, though not all, of the benefits of using the entire genome as a decoy sequence.
+
+* SAF genome index: salmon_sa_index - (the full genome is used as decoy) - The tutorial for creating such an index can be found [here](https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/).  This will result in the largest index, but likely does the best job in avoiding spurious alignments to annotated transcripts. 
+
+**Facing problems with Indexing ?, Check if anyone else already had this problem in the issues section or fill the index generation [request form](https://forms.gle/3baJc5SYrkSWb1z48)**
+
 Chat live about Salmon
 ======================
 
-You can chat with the Salmon developers and other users via Gitter!
+You can chat with the Salmon developers and other users via Gitter (**Note**: Gitter is much less frequently monitored than GitHub, so if you have an important problem or question, please consider opening an issue here on GitHub)!
 
 [![Join the chat at https://gitter.im/COMBINE-lab/salmon](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/COMBINE-lab/salmon?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)