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Title: GitHub - PombertLab/A2A: The A2A pipeline guides users from genome assembly to annotations.

Open Graph Title: GitHub - PombertLab/A2A: The A2A pipeline guides users from genome assembly to annotations.

X Title: GitHub - PombertLab/A2A: The A2A pipeline guides users from genome assembly to annotations.

Description: The A2A pipeline guides users from genome assembly to annotations. - PombertLab/A2A

Open Graph Description: The A2A pipeline guides users from genome assembly to annotations. - PombertLab/A2A

X Description: The A2A pipeline guides users from genome assembly to annotations. - PombertLab/A2A

Opengraph URL: https://github.com/PombertLab/A2A

X: @github

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orient_fastas_to_reference.pyhttps://patch-diff.githubusercontent.com/PombertLab/A2A/blob/main/orient_fastas_to_reference.py
parseTaxonomizedBLAST.plhttps://patch-diff.githubusercontent.com/PombertLab/A2A/blob/main/parseTaxonomizedBLAST.pl
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process_fasta_sequences.pyhttps://patch-diff.githubusercontent.com/PombertLab/A2A/blob/main/process_fasta_sequences.py
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prodigal_to_apollo_gff.pyhttps://patch-diff.githubusercontent.com/PombertLab/A2A/blob/main/prodigal_to_apollo_gff.py
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https://patch-diff.githubusercontent.com/PombertLab/A2A#version-022
https://patch-diff.githubusercontent.com/PombertLab/A2A#updated-2023-06-23
https://patch-diff.githubusercontent.com/PombertLab/A2A#a2a---assembly-to-apollo-annotations
A2GBhttps://github.com/PombertLab/A2GB
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https://patch-diff.githubusercontent.com/PombertLab/A2A#table-of-contents
Requirementshttps://patch-diff.githubusercontent.com/PombertLab/A2A#Requirements
Pipeline Processhttps://patch-diff.githubusercontent.com/PombertLab/A2A#Pipeline-Process
Cleaning Raw Assemblyhttps://patch-diff.githubusercontent.com/PombertLab/A2A#Cleaning-Raw-Assembly
Size Selectionhttps://patch-diff.githubusercontent.com/PombertLab/A2A#Size-Selection
Identify and Remove Contaminantshttps://patch-diff.githubusercontent.com/PombertLab/A2A#Identify-and-Remove-Contaminants
Prepare Apollo for Annotationshttps://patch-diff.githubusercontent.com/PombertLab/A2A#Prepare-Apollo-for-Annotations
Creating an Organismhttps://patch-diff.githubusercontent.com/PombertLab/A2A#Creating-an-Organism
Create and Load Prediction Data as Annotationshttps://patch-diff.githubusercontent.com/PombertLab/A2A#Create-and-Load-Prediction-Data-as-Annotations
Create and Load Referenceshttps://patch-diff.githubusercontent.com/PombertLab/A2A#Create-and-Load-References
Literaturehttps://patch-diff.githubusercontent.com/PombertLab/A2A#Literature
https://patch-diff.githubusercontent.com/PombertLab/A2A#requirements
PERL5https://www.perl.org/
NCBI BLAST+https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Non-Redundant Nucleotide Databasehttps://www.ncbi.nlm.nih.gov/books/NBK62345/#blast_ftp_site.The_blastdb_subdirectory
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https://patch-diff.githubusercontent.com/PombertLab/A2A#pipeline-process
https://patch-diff.githubusercontent.com/PombertLab/A2A#cleaning-raw-assembly
nonredundant nucleotide sequences in NCBIhttps://www.ncbi.nlm.nih.gov/books/NBK62345/#blast_ftp_site.The_blastdb_subdirectory
https://patch-diff.githubusercontent.com/PombertLab/A2A#size-selection
process_fasta_sequences.pyhttps://github.com/PombertLab/A2A/blob/main/process_fasta_sequences.py
https://patch-diff.githubusercontent.com/PombertLab/A2A#identify-and-remove-contaminants
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https://patch-diff.githubusercontent.com/PombertLab/A2A#prepare-apollo-for-annotations
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https://patch-diff.githubusercontent.com/PombertLab/A2A#creating-an-organism
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https://patch-diff.githubusercontent.com/PombertLab/A2A#create-and-load-prediction-data-as-annotations
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https://patch-diff.githubusercontent.com/PombertLab/A2A#create-and-load-references
https://patch-diff.githubusercontent.com/PombertLab/A2A#literature
10.1016/S0022-2836(05)80360-2https://doi.org/10.1016/s0022-2836(05)80360-2
10.1186/1471-2105-11-119https://doi.org/10.1186/1471-2105-11-119
10.1093/nar/gkr1163https://doi.org/10.1093/nar/gkr1163
10.1371/journal.pcbi.1006790https://doi.org/10.1371/journal.pcbi.1006790
doi: 10.1093/nargab/lqaa026https://doi.org/10.1093/nargab/lqaa026
doi: 10.1093/bioinformatics/btn013https://doi.org/10.1093/bioinformatics/btn013
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