Updated User Guide and README for major release v1.0.1

README.md

@@ -2,34 +2,44 @@
 ### End-guided transcriptome assembly.  
 Bookend is a comprehensive framework for end-guided assembly of short-read, long-read, and end-capture RNA-seq data.
 Please see the [User Guide](Bookend_User_Guide.pdf) for a full description of the subcommands and arguments.
+The lastest developments can be found in the [Bookend GitHub repository](https://github.com/Gregor-Mendel-Institute/bookend).
 
 ## Installation  
-Bookend can be installed through the Python Package Index (PyPI) on UNIX systems with Python 3.6+ using the command  
-    pip install bookend-rna
+Bookend can be installed through the Python Package Index (PyPI) on UNIX systems with Python 3.6+ using the command:
+```
+pip install bookend-rna
+```
 
-Once installed, all utilities can be accessed on the command as bookend subcommands:  
-
-usage: bookend [subcommand] [options] [input file(s)]
-Subcommands (use -h/--help for more info):
-
-    label    (Label 5' and 3' ends in a FASTQ file)
-    assemble (Assemble transcripts from aligned end-labeled reads)
-    merge    (Merge assembled GTFs with a reference annotation)
+If installing from the GitHub source code, perform the following steps:
+```
+git clone https://github.com/Gregor-Mendel-Institute/bookend
+cd bookend
+python3 setup.py install
+```
 
-    --end-labeled read (ELR) operations--
-    make-elr
-    sort-elr
-    combine-elr
+Once installed, all utilities can be accessed on the command as bookend subcommands:  
+
+    usage: bookend [subcommand] [options] [input file(s)]
+    Subcommands (use -h/--help for more info):
 
-    --file conversion--
-    bed-to-elr
-    elr-to-bed
-    gtf-to-bed
-    sam-to-sj
-    sj-to-bed
-    sj-merge
+        label    (Label 5' and 3' ends in a FASTQ file)
+        elr      (Convert a BAM/SAM file to the end-labeled read format)
+        assemble (Assemble transcripts from aligned end-labeled reads)
+        condense (Partial assembly that leaves keeps all fragments; use for meta-assembly)
+        classify (Compare an assembly to the transcripts of a reference annotation)
+        bedgraph (Write a coverage Bedgraph file of end-labeled reads)
+        fasta    (Write a transcript FASTA file from an annotation and genome)
 
-    --setup/indexing--
-    index-fasta
-    softbridge-fasta
-
+        --end-labeled read (ELR) operations--
+        elr-sort
+        elr-subset
+        elr-combine
+        
+        --file conversion--
+        gtf-to-bed
+        gtf-ends
+        bed-to-elr
+        elr-to-bed
+        sam-to-sj
+        sj-to-bed
+        sj-merge

bookend/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '1.0.0'
+__version__ = '1.0.1'
 __updated__ = '04.25.2022'
 __date__ = '04.25.2022'

setup.py

@@ -38,7 +38,7 @@ def run(self):
 
 setup(
     name="bookend_rna", # Replace with your own username
-    version="1.0.0",
+    version="1.0.1",
     author="Michael A. Schon",
     author_email="[email protected]",
     description="End-guided transcript assembler for short and long RNA-seq reads.",