diff --git a/README.md b/README.md
index 2848d90..1925fe4 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
-[](https://doi.org/10.5281/zenodo.17094657)
+[](https://doi.org/10.5281/zenodo.15616299)
[](https://anaconda.org/samtobam/stargraph)
[](https://anaconda.org/samtobam/stargraph)
[](https://anaconda.org/samtobam/stargraph)
@@ -107,7 +107,7 @@ the _Starship_ annotations (_starfish_output/elementFinder/\*.elements.ann.feat_
pggb specific inputs:
-pi | --identity -p option in pggb (Default: Automatically calulated using mash distances)
- -l | --length -s option in pggb (Default: 20000 ; a conservative value increased from default pggb values)
+ -l | --length -s option in pggb (Default: 10000 ; a mildly conservative value increased from default pggb values)
-k | --kmersize -k option in pggb (Default: 19 ; same as pggb)
-G | --poaparam -G option in pggb (Default: 7919,8069; a conservative value increased from default pggb values)
@@ -127,14 +127,19 @@ the _Starship_ annotations (_starfish_output/elementFinder/\*.elements.ann.feat_
The final output **_stargraph_output/${prefix}.starships_SLRs.tsv_** contains the final results of ```stargraph```; a nonredundant list of _Starships_ and _Starship_-like elements
Additionally:
-**1.*.pggb** : all genome-graph output from both pggb and odgi
- information about the identified regions of Presence/Absence variation
-**2.PAVs_to_SLRs** : information on the elevation of PAVs to SLRs using the provided tyrosine recombinase locations
- contains information on the elevation of PAVs not elevated to SLR status but containing DUF3723 or MYB genes
-**3.SLR_plots** : plots showing the alignment of SLRs clustered based on k-mer max-containment, including one insertion site per cluster
-**4.SLR_starship_combination** : information on generating the non-redundant dataset combining the provided _Starships_ with the newly identified SLRs
-**5.SLR_starship_network_alignments** : plots showing the alignment of _Starships_ and SLRs clustered together based on k-mer max-containment
- plots of networks using both Jaccard similarity and containment
+**1.*.pggb** :
+All genome-graph output from both pggb and odgi
+Information about the identified regions of Presence/Absence variation
+**2.PAVs_to_SLRs** :
+Information on the elevation of PAVs to SLRs using the provided tyrosine recombinase locations
+Information on the elevation of PAVs not elevated to SLR status but containing DUF3723 or MYB genes
+**3.SLR_plots** :
+Plots showing the alignment of SLRs clusters, including one insertion site per cluster
+**4.SLR_starship_combination** :
+Information on generating the non-redundant dataset combining the provided _Starships_ with the newly identified SLRs
+**5.SLR_starship_network_alignments** :
+Plots showing the alignment of the combined _Starships_ and SLRs clusters
+Plots of networks using both Jaccard similarity and containment
# COMING SOON STEP 6 Running allstars
diff --git a/bin/stargraph.sh b/bin/stargraph.sh
index c56234f..c4342cf 100644
--- a/bin/stargraph.sh
+++ b/bin/stargraph.sh
@@ -1,7 +1,7 @@
#!/bin/bash
set -euo pipefail
-version="v1.0.0"
+version="v1.0.1"
#####################################################################################
############# STEP -1. CREATING THE ENVIRONMENT. NOT ACTUALLY USED NOW ##############
@@ -58,7 +58,7 @@ elements=""
threads="1"
identifier="tyr"
identity=""
-length="20000"
+length="10000"
kmersize="19"
separator="_"
window="1000"
@@ -189,7 +189,7 @@ case "$key" in
pggb specific inputs:
-pi | --identity -p option in pggb (Default: Automatically calulated using mash distances)
- -l | --length -s option in pggb (Default: 20000 ; a conservative value increased from default pggb values)
+ -l | --length -s option in pggb (Default: 10000 ; a mildly conservative value increased from default pggb values)
-k | --kmersize -k option in pggb (Default: 19 ; same as pggb)
-G | --poaparam -G option in pggb (Default: 7919,8069; a conservative value increased from default pggb values)
@@ -308,7 +308,8 @@ genomecount=$( cat path_to_assemblies.txt | wc -l )
samtools faidx ${prefix}.assemblies.fa.gz
##now build the genome graph
-pggb -i ${prefix}.assemblies.fa.gz -o 1.${prefix}.pggb -t ${threads} -p ${identity} -s ${length} -m -S -n ${genomecount} -k ${kmersize} -Y ${separator} -G ${poaparam}
+pggb -i ${prefix}.assemblies.fa.gz -o 1.${prefix}.pggb -t ${threads} -p ${identity} -s ${length} -m -S -n ${genomecount} -k ${kmersize} -Y ${separator} -G ${poaparam} > pggb.log
+mv pggb.log 1.${prefix}.pggb
##move in the output folder so we can try use this graph to extract Starship regions
cd 1.${prefix}.pggb
@@ -944,6 +945,9 @@ done
cd ..
+
+echo "Stargraph complete; E noho rā"
+
######################################################################################################################################################################################################################################
######################################################################################################################################################################################################################################
######################################################################################################################################################################################################################################
diff --git a/meta.yaml b/meta.yaml
index 407d8b8..ec7027b 100644
--- a/meta.yaml
+++ b/meta.yaml
@@ -1,6 +1,6 @@
package:
name: stargraph
- version: "1.0.0" # Change this to your desired version
+ version: "1.0.1" # Change this to your desired version
source:
git_url: https://github.com/samtobam/stargraph.git