From fc00abc0de60938be364661e06c3de6f64f5ec30 Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Sat, 11 Apr 2026 03:13:20 -0500 Subject: [PATCH 1/8] Superficial update --- README.md | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 2848d90..8d401d1 100644 --- a/README.md +++ b/README.md @@ -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 From b30c05e279f9a49a9a39ed23fa340bfedeebd109 Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Sat, 11 Apr 2026 03:19:23 -0500 Subject: [PATCH 2/8] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8d401d1..2ace5a8 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@

-[![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) From ca963cdde4b4ce93e3826acb163618b16178864b Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Sun, 12 Apr 2026 12:56:58 -0500 Subject: [PATCH 3/8] Update stargraph.sh --- bin/stargraph.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/bin/stargraph.sh b/bin/stargraph.sh index c56234f..1b200b0 100644 --- a/bin/stargraph.sh +++ b/bin/stargraph.sh @@ -944,6 +944,9 @@ done cd .. + +echo "Stargraph complete; E noho rā" + ###################################################################################################################################################################################################################################### ###################################################################################################################################################################################################################################### ###################################################################################################################################################################################################################################### From d374a15c0a602792f11ef966d1602a35629de76d Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Sun, 12 Apr 2026 15:08:26 -0500 Subject: [PATCH 4/8] Update stargraph.sh send stdout output from pggb to log file then move into pggb output folder --- bin/stargraph.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/stargraph.sh b/bin/stargraph.sh index 1b200b0..2808677 100644 --- a/bin/stargraph.sh +++ b/bin/stargraph.sh @@ -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.${prefix}.pggb From 14dcf9a8edc803da47c37a65abffa2295b46d009 Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Mon, 13 Apr 2026 08:19:03 -0500 Subject: [PATCH 5/8] reduce default -l parameter from 20-10k --- bin/stargraph.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/stargraph.sh b/bin/stargraph.sh index 2808677..b5cf39d 100644 --- a/bin/stargraph.sh +++ b/bin/stargraph.sh @@ -58,7 +58,7 @@ elements="" threads="1" identifier="tyr" identity="" -length="20000" +length="10000" kmersize="19" separator="_" window="1000" @@ -189,7 +189,7 @@ case "$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) From 98b7c79f7e19719eb74bfc790a655e5a055843f0 Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Mon, 13 Apr 2026 08:19:14 -0500 Subject: [PATCH 6/8] Update stargraph.sh --- bin/stargraph.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/stargraph.sh b/bin/stargraph.sh index b5cf39d..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 ############## From 05eaf750daf17ff30ce40245c4ccd29cad3908de Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Mon, 13 Apr 2026 08:19:36 -0500 Subject: [PATCH 7/8] Update meta.yaml --- meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 34fa823956f57f2a3f2c160b224dbefb100ee2f5 Mon Sep 17 00:00:00 2001 From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com> Date: Mon, 13 Apr 2026 08:20:17 -0500 Subject: [PATCH 8/8] update readme help message --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2ace5a8..1925fe4 100644 --- a/README.md +++ b/README.md @@ -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)