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kakapo: easy extraction and annotation of genes from raw RNA-seq reads

kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline id...

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Detalles Bibliográficos
Autores principales: Ramanauskas, Karolis, Igić, Boris
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688300/
https://www.ncbi.nlm.nih.gov/pubmed/38034874
http://dx.doi.org/10.7717/peerj.16456
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author Ramanauskas, Karolis
Igić, Boris
author_facet Ramanauskas, Karolis
Igić, Boris
author_sort Ramanauskas, Karolis
collection PubMed
description kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed for targeted assembly, to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of GenBank’s single-gene databases and help assemble datasets for a variety of phylogenetic analyses.
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spelling pubmed-106883002023-11-30 kakapo: easy extraction and annotation of genes from raw RNA-seq reads Ramanauskas, Karolis Igić, Boris PeerJ Bioinformatics kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed for targeted assembly, to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of GenBank’s single-gene databases and help assemble datasets for a variety of phylogenetic analyses. PeerJ Inc. 2023-11-27 /pmc/articles/PMC10688300/ /pubmed/38034874 http://dx.doi.org/10.7717/peerj.16456 Text en ©2023 Ramanauskas and Igić https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Ramanauskas, Karolis
Igić, Boris
kakapo: easy extraction and annotation of genes from raw RNA-seq reads
title kakapo: easy extraction and annotation of genes from raw RNA-seq reads
title_full kakapo: easy extraction and annotation of genes from raw RNA-seq reads
title_fullStr kakapo: easy extraction and annotation of genes from raw RNA-seq reads
title_full_unstemmed kakapo: easy extraction and annotation of genes from raw RNA-seq reads
title_short kakapo: easy extraction and annotation of genes from raw RNA-seq reads
title_sort kakapo: easy extraction and annotation of genes from raw rna-seq reads
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688300/
https://www.ncbi.nlm.nih.gov/pubmed/38034874
http://dx.doi.org/10.7717/peerj.16456
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