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Superficial update #12

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fc00abc
Superficial update
SAMtoBAM Apr 11, 2026
b30c05e
Update README.md
SAMtoBAM Apr 11, 2026
ca963cd
Update stargraph.sh
SAMtoBAM Apr 12, 2026
d374a15
Update stargraph.sh
SAMtoBAM Apr 12, 2026
14dcf9a
reduce default -l parameter from 20-10k
SAMtoBAM Apr 13, 2026
98b7c79
Update stargraph.sh
SAMtoBAM Apr 13, 2026
05eaf75
Update meta.yaml
SAMtoBAM Apr 13, 2026
34fa823
update readme help message
SAMtoBAM Apr 13, 2026
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25 changes: 15 additions & 10 deletions README.md
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Expand Up @@ -2,7 +2,7 @@
<img src="https://github.com/SAMtoBAM/stargraph/blob/main/logo/stargraph_logo.png" width=100%>
</p>

[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17094657.svg)](https://doi.org/10.5281/zenodo.17094657)
[![Zenodo DOI](https://zenodo.org/badge/992224579.svg)](https://doi.org/10.5281/zenodo.15616299)
[![Anaconda_version](https://anaconda.org/samtobam/stargraph/badges/version.svg)](https://anaconda.org/samtobam/stargraph)
[![Anaconda_platforms](https://anaconda.org/samtobam/stargraph/badges/platforms.svg)](https://anaconda.org/samtobam/stargraph)
[![Anaconda_downloads](https://anaconda.org/samtobam/stargraph/badges/downloads.svg)](https://anaconda.org/samtobam/stargraph)
Expand Down Expand Up @@ -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)

Expand All @@ -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 <br/>
Additionally: <br/>
**1.*.pggb** : all genome-graph output from both pggb and odgi <br/>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; information about the identified regions of Presence/Absence variation <br/>
**2.PAVs_to_SLRs** : information on the elevation of PAVs to SLRs using the provided tyrosine recombinase locations <br/>
&nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; contains information on the elevation of PAVs not elevated to SLR status but containing DUF3723 or MYB genes <br/>
**3.SLR_plots** : plots showing the alignment of SLRs clustered based on k-mer max-containment, including one insertion site per cluster <br/>
**4.SLR_starship_combination** : information on generating the non-redundant dataset combining the provided _Starships_ with the newly identified SLRs <br/>
**5.SLR_starship_network_alignments** : plots showing the alignment of _Starships_ and SLRs clustered together based on k-mer max-containment <br/>
&nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; plots of networks using both Jaccard similarity and containment <br/>
**1.*.pggb** : <br/>
All genome-graph output from both pggb and odgi <br/>
Information about the identified regions of Presence/Absence variation <br/>
**2.PAVs_to_SLRs** : <br/>
Information on the elevation of PAVs to SLRs using the provided tyrosine recombinase locations <br/>
Information on the elevation of PAVs not elevated to SLR status but containing DUF3723 or MYB genes <br/>
**3.SLR_plots** : <br/>
Plots showing the alignment of SLRs clusters, including one insertion site per cluster <br/>
**4.SLR_starship_combination** : <br/>
Information on generating the non-redundant dataset combining the provided _Starships_ with the newly identified SLRs <br/>
**5.SLR_starship_network_alignments** : <br/>
Plots showing the alignment of the combined _Starships_ and SLRs clusters <br/>
Plots of networks using both Jaccard similarity and containment <br/>


# COMING SOON STEP 6 Running allstars
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12 changes: 8 additions & 4 deletions bin/stargraph.sh
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@@ -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 ##############
Expand Down Expand Up @@ -58,7 +58,7 @@ elements=""
threads="1"
identifier="tyr"
identity=""
length="20000"
length="10000"
kmersize="19"
separator="_"
window="1000"
Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -944,6 +945,9 @@ done

cd ..


echo "Stargraph complete; E noho rā"

######################################################################################################################################################################################################################################
######################################################################################################################################################################################################################################
######################################################################################################################################################################################################################################
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2 changes: 1 addition & 1 deletion meta.yaml
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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
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