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33A viewer for multiple alignment format (MAF) files in JBrowse 2
44
5- This is a port of the JBrowse 1 plugin https://github.com/cmdcolin/mafviewer to
6- JBrowse 2
7-
85![ ] ( img/1.png )
96
107## Demo
@@ -15,9 +12,12 @@ https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fmaf%2Fhg38%2Fdistconfig.jso
1512
1613This plugin supports three input formats:
1714
18- 1 . ** BigMaf** - UCSC BigMaf format (.bb files)
15+ 1 . ** BigMaf** - UCSC BigMaf format e.g. .bb/.bigMaf
16+ (https://genome.ucsc.edu/goldenpath/help/bigMaf.html )
19172 . ** MAF tabix** - bgzip-compressed MAF converted to BED format with tabix index
18+ (a custom format we created, more info in this README)
20193 . ** TAF (Taffy)** - bgzip-compressed TAF format with .tai index
20+ (https://github.com/ComparativeGenomicsToolkit/taffy )
2121
2222## GUI usage (e.g. in JBrowse Desktop)
2323
@@ -41,7 +41,7 @@ Then use the custom "Add track workflow":
4141 "plugins" : [
4242 {
4343 "name" : " MafViewer" ,
44- "url" : " https://unpkg.com /jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
44+ "url" : " https://jbrowse.org/plugins /jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
4545 }
4646 ]
4747}
@@ -260,3 +260,8 @@ short alignment blocks:
260260taffy view -i file.maf | taffy norm | bgzip > out.taf.gz
261261taffy index -i out.taf.gz
262262```
263+
264+ ## Footnote
265+
266+ This is a port of the JBrowse 1 plugin https://github.com/cmdcolin/mafviewer to
267+ JBrowse 2
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