RGFA: powerful and convenient handling of assembly graphs
The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to...
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| Format: | Online |
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PeerJ Inc.
2016
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103826/ |
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pubmed-51038262016-11-14 RGFA: powerful and convenient handling of assembly graphs Gonnella, Giorgio Kurtz, Stefan Bioinformatics The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA can be employed to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g., to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs. PeerJ Inc. 2016-11-08 /pmc/articles/PMC5103826/ /pubmed/27843717 http://dx.doi.org/10.7717/peerj.2681 Text en ©2016 Gonnella and Kurtz http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://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. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Gonnella, Giorgio Kurtz, Stefan |
| spellingShingle |
Gonnella, Giorgio Kurtz, Stefan RGFA: powerful and convenient handling of assembly graphs |
| author_facet |
Gonnella, Giorgio Kurtz, Stefan |
| author_sort |
Gonnella, Giorgio |
| title |
RGFA: powerful and convenient handling of assembly graphs |
| title_short |
RGFA: powerful and convenient handling of assembly graphs |
| title_full |
RGFA: powerful and convenient handling of assembly graphs |
| title_fullStr |
RGFA: powerful and convenient handling of assembly graphs |
| title_full_unstemmed |
RGFA: powerful and convenient handling of assembly graphs |
| title_sort |
rgfa: powerful and convenient handling of assembly graphs |
| description |
The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA can be employed to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g., to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs. |
| publisher |
PeerJ Inc. |
| publishDate |
2016 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103826/ |
| _version_ |
1613721449233645568 |