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Title: GitHub - PombertLab/A2GB: A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank.

Open Graph Title: GitHub - PombertLab/A2GB: A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank.

X Title: GitHub - PombertLab/A2GB: A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank.

Description: A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank. - GitHub - PombertLab/A2GB: A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank.

Open Graph Description: A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank. - GitHub - PombertLab/A2GB: A2GB is a pipeline tha...

X Description: A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank. - GitHub - PombertLab/A2GB: A2GB is a pipeline tha...

Opengraph URL: https://github.com/PombertLab/A2GB

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LICENSEhttps://github.com/PombertLab/A2GB/blob/master/LICENSE
LICENSEhttps://github.com/PombertLab/A2GB/blob/master/LICENSE
README.mdhttps://github.com/PombertLab/A2GB/blob/master/README.md
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check_problems.plhttps://github.com/PombertLab/A2GB/blob/master/check_problems.pl
READMEhttps://github.com/PombertLab/A2GB
MIT licensehttps://github.com/PombertLab/A2GB
https://github.com/PombertLab/A2GB#a2gb--annotations-to-genbank
https://zenodo.org/doi/10.5281/zenodo.5532811
A2GBhttps://github.com/PombertLab/A2GB/
Apollohttps://genomearchitect.readthedocs.io/en/latest/
WebApollohttp://gmod.org/wiki/WebApollo
GenBankhttps://www.ncbi.nlm.nih.gov/genbank/
NCBI’s guidelineshttps://www.ncbi.nlm.nih.gov/genbank/genomesubmit/
BioSamplehttps://www.ncbi.nlm.nih.gov/biosample
BioProjecthttps://www.ncbi.nlm.nih.gov/bioproject
locus_taghttps://www.ncbi.nlm.nih.gov/genomes/locustag/Proposal.pdf
International Nucleotide Sequence Database Collaborationhttp://www.insdc.org/
https://github.com/PombertLab/A2GB#table-of-contents
Introductionhttps://github.com/PombertLab/A2GB#introduction
Requirementshttps://github.com/PombertLab/A2GB#requirements
A2GB workflowhttps://github.com/PombertLab/A2GB#A2GB-workflow
Exporting annotations from Apollohttps://github.com/PombertLab/A2GB#Exporting-annotations-from-Apollo
Splitting Apollo GFF3 fileshttps://github.com/PombertLab/A2GB#Splitting-Apollo-GFF3-files
Converting GFF3 files to EMBL formathttps://github.com/PombertLab/A2GB#Converting-GFF3-files-to-EMBL-format
Checking for internal stop codons and missing start methionineshttps://github.com/PombertLab/A2GB#Checking-for-internal-stop-codons-and-missing-start-methionines
Creating tab-delimited lists of RNA locus tags and their productshttps://github.com/PombertLab/A2GB#Creating-tab-delimited-lists-of-RNA-locus-tags-and-their-products
Protein function predictionhttps://github.com/PombertLab/A2GB#Protein-function-prediction
Predicting functions with InterProScan5https://github.com/PombertLab/A2GB#Predicting-functions-with-InterProScan5
Performing homology searches against UniProt databaseshttps://github.com/PombertLab/A2GB#Performing-homology-searches-against-UniProt-databases
Downloading the SwissProt and TrEMBL databaseshttps://github.com/PombertLab/A2GB#Downloading-the-SwissProt-and-TrEMBL-databases
Creating tab-delimited product lists from UniProt databaseshttps://github.com/PombertLab/A2GB#Creating-tab-delimited-product-lists-from-UniProt-databases
Running DIAMOND or BLAST searches against UniProt databaseshttps://github.com/PombertLab/A2GB#Running-DIAMOND-or-BLAST-searches-against-UniProt-databases
Performing homology searches against reference datasetshttps://github.com/PombertLab/A2GB#Performing-homology-searches-against-reference-datasets
Searching KEGG databases for orthologshttps://github.com/PombertLab/A2GB#Searching-KEGG-databases-for-orthologs
Parsing the results from homology searcheshttps://github.com/PombertLab/A2GB#Parsing-the-results-from-homology-searches
Curating the protein annotationshttps://github.com/PombertLab/A2GB#Curating-the-protein-annotations
Converting EMBL files to ASN formathttps://github.com/PombertLab/A2GB#Converting-EMBL-files-to-ASN-format
Converting EMBL files to TBL formathttps://github.com/PombertLab/A2GB#Converting-EMBL-files-to-TBL-format
Converting TBL files to ASN formathttps://github.com/PombertLab/A2GB#Converting-TBL-files-to-ASN-format
Adding metadata to FASTA fileshttps://github.com/PombertLab/A2GB#Adding-metadata-to-FASTA-files
Generating a GenBank submission templatehttps://github.com/PombertLab/A2GB#Generating-a-GenBank-submission-template
Creating structured commentshttps://github.com/PombertLab/A2GB#Creating-structured-comments
Using table2asnhttps://github.com/PombertLab/A2GB#Using-table2asn
Checking for errors and fixing themhttps://github.com/PombertLab/A2GB#Checking-for-errors-and-fixing-them
Partial geneshttps://github.com/PombertLab/A2GB#Partial-genes
Missing stop codons and GT-AG splice siteshttps://github.com/PombertLab/A2GB#Missing-stop-codons-and-GT-AG-splice-sites
Fixing errorshttps://github.com/PombertLab/A2GB#Fixing-errors
Submitting ASN files to GenBankhttps://github.com/PombertLab/A2GB#Submitting-ASN-files-to-GenBank
Funding and acknowledgmentshttps://github.com/PombertLab/A2GB#Funding-and-acknowledgments
Referenceshttps://github.com/PombertLab/A2GB#References
https://github.com/PombertLab/A2GB#introduction
Apollohttps://genomearchitect.readthedocs.io/en/latest/
GenBankhttps://www.ncbi.nlm.nih.gov/genbank/
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Apollohttps://genomearchitect.readthedocs.io/en/latest/
NCBIhttps://www.ncbi.nlm.nih.gov/
UniProthttps://www.uniprot.org/
InterProhttps://www.ebi.ac.uk/interpro/
https://github.com/PombertLab/A2GB#requirements
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Perl 5https://www.perl.org/
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RNAmmerhttps://services.healthtech.dtu.dk/software.php
tRNAscan-SEhttp://lowelab.ucsc.edu/tRNAscan-SE/
Artemishttp://sanger-pathogens.github.io/Artemis/Artemis/
aria2https://aria2.github.io/
InterProScan 5https://github.com/ebi-pf-team/interproscan
DIAMONDhttps://github.com/bbuchfink/diamond
NCBI BLAST+https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
ChimeraXhttps://www.cgl.ucsf.edu/chimerax/download.html
https://github.com/PombertLab/A2GB#a2gb-workflow
https://github.com/PombertLab/A2GB#exporting-annotations-from-apollo
https://github.com/PombertLab/A2GB/blob/master/Misc/Apollo.png
https://github.com/PombertLab/A2GB/blob/master/Misc/Apollo2.png
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tRNAscan_to_GFF3.plhttps://github.com/PombertLab/A2GB/blob/master/Apollo_tools/tRNAscan_to_GFF3.pl
https://github.com/PombertLab/A2GB#splitting-apollo-gff3-files
Artemishttp://sanger-pathogens.github.io/Artemis/Artemis/
splitGFF3.plhttps://github.com/PombertLab/A2GB/blob/master/Apollo_tools/splitGFF3.pl
https://github.com/PombertLab/A2GB#converting-gff3-files-to-embl-format
locus_tag prefixhttps://www.ncbi.nlm.nih.gov/genomes/locustag/Proposal.pdf
BioSamplehttps://www.ncbi.nlm.nih.gov/biosample
BioProjecthttps://www.ncbi.nlm.nih.gov/bioproject
NCBIhttps://www.ncbi.nlm.nih.gov/
EMBL-EBIhttps://www.ebi.ac.uk/
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Artemishttp://sanger-pathogens.github.io/Artemis/Artemis/
https://github.com/PombertLab/A2GB/blob/master/Misc/Artemis.png
https://github.com/PombertLab/A2GB#checking-for-internal-stop-codons-and-missing-start-methionines
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Apollohttps://genomearchitect.readthedocs.io/en/latest/
Artemishttp://sanger-pathogens.github.io/Artemis/Artemis/
https://github.com/PombertLab/A2GB/blob/master/Misc/Artemis_2.png
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EMBLtoFeatures.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoFeatures.pl
https://github.com/PombertLab/A2GB#creating-tab-delimited-lists-of-rna-locus-tags-and-their-products
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sectionhttps://github.com/PombertLab/A2GB/blob/master/README.md#Exporting-annotations-from-Apollo
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https://github.com/PombertLab/A2GB#protein-function-prediction
InterProScan 5https://github.com/ebi-pf-team/interproscan
BLASTPhttps://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
DIAMONDhttps://github.com/bbuchfink/diamond
UniProthttps://www.uniprot.org/
BLASTPhttps://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
DIAMONDhttps://github.com/bbuchfink/diamond
https://github.com/PombertLab/A2GB#predicting-functions-with-interproscan5
InterProhttps://www.ebi.ac.uk/interpro/
InterProScan 5https://github.com/ebi-pf-team/interproscan
run_InterProScan.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/run_InterProScan.pl
run_InterProScan.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/run_InterProScan.pl
run_InterProScan.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/run_InterProScan.pl
sectionhttps://github.com/PombertLab/A2GB/blob/master/README.md#checking-for-internal-stop-codons-and-missing-start-methionines
https://github.com/PombertLab/A2GB#performing-homology-searches-against-uniprot-databases
UniProthttps://www.uniprot.org/
NCBI BLAST+https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
DIAMONDhttps://github.com/bbuchfink/diamond
DIAMONDhttps://github.com/bbuchfink/diamond
https://github.com/PombertLab/A2GB#downloading-the-swissprot-and-trembl-databases
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aria2https://aria2.github.io/
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https://github.com/PombertLab/A2GB#creating-tab-delimited-product-lists-from-uniprot-databases
UniProthttps://www.uniprot.org/
get_uniprot_products.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/get_uniprot_products.pl
https://github.com/PombertLab/A2GB#running-diamond-or-blast-searches-against-uniprot-databases
DIAMONDhttps://github.com/bbuchfink/diamond
UniProthttps://www.uniprot.org/
herehttps://github.com/bbuchfink/diamond/wiki
NCBI BLAST+https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
https://github.com/PombertLab/A2GB#performing-homology-searches-against-reference-datasets
NCBI genomehttps://www.ncbi.nlm.nih.gov/genome
datasethttps://www.ncbi.nlm.nih.gov/datasets/genomes/
get_reference_products.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/get_reference_products.pl
https://github.com/PombertLab/A2GB#searching-kegg-databases-for-orthologs
Kyoto Encyclopedia of Genes and Genomeshttps://www.genome.jp/kegg/
BlastKOALAhttps://www.kegg.jp/blastkoala/
GhostKOALAhttps://www.kegg.jp/ghostkoala/
KofamKOALAhttps://www.genome.jp/tools/kofamkoala/
https://github.com/PombertLab/A2GB#parsing-the-results-from-homology-searches
get_queries.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/get_queries.pl
get_queries.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/get_queries.pl
get_uniprot_products.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/get_uniprot_products.pl
parse_annotators.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/parse_annotators.pl
parse_annotators.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/parse_annotators.pl
parse_annotators.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/parse_annotators.pl
KEGGhttps://www.genome.jp/kegg/
dbCAN2http://bcb.unl.edu/dbCAN2/
parse_annotators.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/parse_annotators.pl
https://github.com/PombertLab/A2GB#curating-the-protein-annotations
curate_annotations.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/curate_annotations.pl
parse_annotators.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/parse_annotators.pl
curate_annotations.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/curate_annotations.pl
curate_annotations.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/curate_annotations.pl
curate_annotations.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/curate_annotations.pl
curate_annotations.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/curate_annotations.pl
curate_annotations.plhttps://github.com/PombertLab/A2GB/blob/master/Function_prediction/curate_annotations.pl
https://github.com/PombertLab/A2GB#converting-embl-files-to-asn-format
A2GBhttps://github.com/PombertLab/A2GB
EMBLtoTBL.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoTBL.pl
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
https://github.com/PombertLab/A2GB#converting-embl-files-to-tbl-format
EMBLtoTBL.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoTBL.pl
previouslyhttps://github.com/PombertLab/A2GB#Creating-tab-delimited-lists-of-RNA-locus-tags-and-their-products
abovehttps://github.com/PombertLab/A2GB#curating-the-protein-annotations
EMBLtoTBL.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoTBL.pl
EMBLtoTBL.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoTBL.pl
https://github.com/PombertLab/A2GB#converting-tbl-files-to-asn-format
https://github.com/PombertLab/A2GB#adding-metadata-to-fasta-files
herehttps://www.ncbi.nlm.nih.gov/genbank/mods_fastadefline/
add_metadata_to_fasta.plhttps://github.com/PombertLab/A2GB/blob/master/add_metadata_to_fasta.pl
add_metadata_to_fasta.plhttps://github.com/PombertLab/A2GB/blob/master/add_metadata_to_fasta.pl
add_metadata_to_fasta.plhttps://github.com/PombertLab/A2GB/blob/master/add_metadata_to_fasta.pl
metakeys_NCBI.tsvhttps://github.com/PombertLab/A2GB/blob/master/Example_files/metakeys_NCBI.tsv
chromosomes.tsvhttps://github.com/PombertLab/A2GB/blob/master/Example_files/chromosomes.tsv
https://github.com/PombertLab/A2GB#generating-a-genbank-submission-template
https://submit.ncbi.nlm.nih.gov/genbank/template/submission/https://submit.ncbi.nlm.nih.gov/genbank/template/submission/
https://github.com/PombertLab/A2GB#creating-structured-comments
herehttps://www.ncbi.nlm.nih.gov/genbank/structuredcomment/
https://github.com/PombertLab/A2GB#using-table2asn
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
GenBankhttps://www.ncbi.nlm.nih.gov/genbank/
EMBLtoTBL.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoTBL.pl
Eukaryotic Genome Annotation Guidehttps://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation/
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
https://github.com/PombertLab/A2GB#checking-for-errors-and-fixing-them
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
https://github.com/PombertLab/A2GB#partial-genes
Artemishttp://sanger-pathogens.github.io/Artemis/Artemis/
EMBLtoTBL.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoTBL.pl
https://github.com/PombertLab/A2GB/blob/master/Misc/Partial_1.png
https://github.com/PombertLab/A2GB/blob/master/Misc/Partial_2.png
https://github.com/PombertLab/A2GB#missing-stop-codons-and-gt-ag-splice-sites
Artemishttp://sanger-pathogens.github.io/Artemis/Artemis/
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
https://github.com/PombertLab/A2GB/blob/master/Misc/Missing_sc_1.png
https://github.com/PombertLab/A2GB/blob/master/Misc/MIssing_sc_2.png
https://github.com/PombertLab/A2GB#fixing-errors
Artemishttp://sanger-pathogens.github.io/Artemis/Artemis/
EMBLtoTBL.plhttps://github.com/PombertLab/A2GB/blob/master/EMBLtoTBL.pl
table2asnhttps://www.ncbi.nlm.nih.gov/genbank/table2asn/
https://github.com/PombertLab/A2GB/blob/master/Misc/Saveas_artemis.png
https://github.com/PombertLab/A2GB#submitting-asn-files-to-genbank
NCBI's genome submission portalhttps://submit.ncbi.nlm.nih.gov/
BioProjecthttps://www.ncbi.nlm.nih.gov/bioproject
BioSamplehttps://www.ncbi.nlm.nih.gov/biosample
https://github.com/PombertLab/A2GB#note
Submitting Multiple Haplotype Assemblieshttps://www.ncbi.nlm.nih.gov/genbank/diploid_haps/
https://github.com/PombertLab/A2GB#funding-and-acknowledgments
https://github.com/PombertLab/A2GB#references
10.1038/nmeth.3176https://doi.org/10.1038/nmeth.3176
10.1016/S0022-2836(05)80360-2https://doi.org/10.1016/s0022-2836(05)80360-2
PMC3245069http://www.ncbi.nlm.nih.gov/pmc/articles/pmc3245069/
10.1093/nar/gkr1163https://doi.org/10.1093/nar/gkr1163
PMC6380598http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6380598/
10.1371/journal.pcbi.1006790https://doi.org/10.1371/journal.pcbi.1006790
PMC3278759http://www.ncbi.nlm.nih.gov/pmc/articles/pmc3278759/
10.1093/bioinformatics/btr703https://doi.org/10.1093/bioinformatics/btr703
PMC6768409http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6768409/
10.1007/978-1-4939-9173-0_1https://doi.org/10.1007/978-1-4939-9173-0_1
PMC1888812http://www.ncbi.nlm.nih.gov/pmc/articles/pmc1888812/
10.1093/nar/gkm160https://doi.org/10.1093/nar/gkm160
PMC3998142http://www.ncbi.nlm.nih.gov/pmc/articles/pmc3998142/
10.1093/bioinformatics/btu031https://doi.org/10.1093/bioinformatics/btu031
PMC6323941http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6323941/
10.1093/nar/gky1100https://doi.org/10.1093/nar/gky1100
PMC6323992http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6323992/
10.1093/nar/gky1049https://doi.org/10.1093/nar/gky1049
PMC7145611http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7145611/
10.1093/nar/gkz956https://doi.org/10.1093/nar/gkz956
10.1038/35080529https://doi.org/10.1038/35080529
10.1038/35080529https://doi.org/10.1038/35080529
PMC6933857http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6933857/
10.1002/pro.3711https://doi.org/10.1002/pro.3711
PMC4123905http://www.ncbi.nlm.nih.gov/pmc/articles/pmc4123905/
10.1371/journal.pone.0103833https://doi.org/10.1371/journal.pone.0103833
PMC7141845http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7141845/
10.1093/bioinformatics/btz859https://doi.org/10.1093/bioinformatics/btz859
PMC6031026http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6031026/
10.1093/nar/gky418https://doi.org/10.1093/nar/gky418
github.com/PombertLab/A2GBhttps://github.com/PombertLab/A2GB
genome-annotation https://github.com/topics/genome-annotation
evidence-based https://github.com/topics/evidence-based
function-prediction https://github.com/topics/function-prediction
Readme https://github.com/PombertLab/A2GB#readme-ov-file
MIT license https://github.com/PombertLab/A2GB#MIT-1-ov-file
Please reload this pagehttps://github.com/PombertLab/A2GB
Activityhttps://github.com/PombertLab/A2GB/activity
Custom propertieshttps://github.com/PombertLab/A2GB/custom-properties
3 starshttps://github.com/PombertLab/A2GB/stargazers
2 watchinghttps://github.com/PombertLab/A2GB/watchers
0 forkshttps://github.com/PombertLab/A2GB/forks
Report repository https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FPombertLab%2FA2GB&report=PombertLab+%28user%29
Releases 3https://github.com/PombertLab/A2GB/releases
A2GB-v0.6.1 Latest Sep 27, 2021 https://github.com/PombertLab/A2GB/releases/tag/0.6.0
+ 2 releaseshttps://github.com/PombertLab/A2GB/releases
Packages 0https://github.com/orgs/PombertLab/packages?repo_name=A2GB
Contributors 2https://github.com/PombertLab/A2GB/graphs/contributors
Please reload this pagehttps://github.com/PombertLab/A2GB
Perl 98.1% https://github.com/PombertLab/A2GB/search?l=perl
Python 1.9% https://github.com/PombertLab/A2GB/search?l=python
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

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