Update README.md

README.md

@@ -7,11 +7,10 @@
 RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:
 
 1. Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~ 2 minutes.
-2. In-tact ordering and orienting of contigs so as to retain original sequence content and any analysis that relies on it. 
-3. Lift-over of gff files from the contig-level assembly to the pseudochromosomes.
+2. In-tact ordering and orienting of contigs. 
+3. Chimeric contig correction.
 4. Structural variant calling with [Assemblytics](http://assemblytics.com/).
-
-RaGOO does not automatically create synteny plots/homology maps, but RaGOO output files can easily passed to visualization tools such as Assemblytics (see "Output Files" below).
+5. Confidence scores associated with the grouping, localization, and orientation for each contig.
 
 ## Installation
 
@@ -23,7 +22,7 @@ RaGOO should install on OSX and most standard flavors of Linux. RaGOO depends on
 2. numpy
 3. [minimap2](https://github.com/lh3/minimap2)
 
-The first two packages will be installed automatically when installing RaGOO. minimap2 is straightforward to install following the instructions on its website.
+The first two packages will be installed automatically when installing RaGOO. minimap2 is straightforward to install following the instructions on its website. Place the minimap2 executable in your path, or specify its location with the -m paramter (see below).
 
 ### Installation
 
@@ -36,30 +35,51 @@ $python setup.py install
 ## Usage
 
 ```
-usage: ragoo.py [-h] [-e <exclude.txt>] [-gff <annotations.gff>] [-m PATH]
-                [-b] [-t 3] [-g 100] [-s]
+usage: ragoo.py [-h] [-e <exclude.txt>] [-m PATH] [-b] [-t 3] [-g 100] [-s]
                 <contigs.fasta> <reference.fasta>
 
 order and orient contigs according to minimap2 alignments to a reference
 
 positional arguments:
-  <contigs.fasta>       fasta file with contigs to be ordered and oriented
-  <reference.fasta>     reference fasta file
+  <contigs.fasta>    fasta file with contigs to be ordered and oriented
+  <reference.fasta>  reference fasta file
 
 optional arguments:
-  -h, --help            show this help message and exit
-  -e <exclude.txt>      single column text file of reference headers to ignore
-  -gff <annotations.gff>
-                        Annotations for lift over
-  -m PATH               path to minimap2 executable
-  -b                    Break chimeric contigs
-  -t 3                  Number of threads when running minimap.
-  -g 100                Gap size for padding in pseudomolecules.
-  -s                    Call structural variants
-```
-
-Note that one can optionally break chimeric contigs and call structural variants. Turning off SV calling can be especially useful for large genomes such as Maize and Human for which minimap2 SAM alignments might take a very long time. 
+  -h, --help         show this help message and exit
+  -e <exclude.txt>   single column text file of reference headers to ignore
+  -m PATH            path to minimap2 executable
+  -b                 Break chimeric contigs
+  -t 3               Number of threads when running minimap.
+  -g 100             Gap size for padding in pseudomolecules.
+  -s                 Call structural variants
+``` 
 
 RaGOO will try to be smart and not redo intermediate analysis already done in previous executions of the pipeline. For example, if the minimap2 alignment files are already present from previous runs, RaGOO will not recreate them. However, RaGOO is not that smart, so be sure to remove any files that you want to replace. To be safe, one can just remove the entire output directory if a new analysis is desired (see "Output Files" below).
 
+### Example Run
+
 ### Output Files
+
+All of the output will be in the "ragoo_output" directory. If breaking chimeric contigs and calling SVs, the contents of this output directory is as follows:
+
+```
+ragoo_output/
+├── chimera_break
+├── groupings
+├── orderings
+└── pm_alignments
+```
+
+#### chimera_break
+This directory cotnains the results from chimeric contig breaking. It contains two alignment (PAF) files of contigs against the reference, one for intrachromosmal and itnerchromosmal chimeras. A new corrected fasta file is also associated with each alignment file.
+
+The most notable file here is the **[prefix].intra.chimera.broken.fa**, as this is the final corrected assembly used for downstream scaffolding. All of the downstream information such as confidence scores refers to this assembly, not the orignal assembly.
+
+#### groupings
+There is one file per chromosome listing the contigs assigned to that chromosome, and their grouping confidenc score. Please not that these contigs are not ordered. Also note that if chimeras were corrected, the headears in these files refer to the broekn assembly in "chimera_break", and not the original assembly.
+
+#### orderings
+There is one file per chromosome showing the ordering, orientation (second column), location confidence scores (third column), and orientation confidence scores (fourth column) for each chromosome.
+
+#### pm_alignments
+This directory contains all of the structural variant calling results. The final structural variants can be found in **assemblytics_out.Assemblytics_structural_variants.bed**. There is also the alignmens of the RaGOO pseudomolecules against the provided reference in both SAM and delta format (**pm_contigs_against_ref.sam** and **pm_contigs_against_ref.sam.delta**).