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ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then processed to generate a pseudomolecule taking overlapping contigs and gaps in to account. ABACAS generates a comparision file that can be used to visualize ordered and oriented contigs in ACT. Synteny is represented by red bars where colour intensity decreases with lower values of percent identity between comparable blocks. Information on contigs such as the orientation, percent identity, coverage and overlap with other contigs can also be visualized by loading the outputted feature file on ACT.
 
Description
ABACAS bruger MUMmer til at finde justeringspositioner og identificere syntenier af samlede contig'er mod referencen. Resultatet behandles så for at oprette et pseudomolekyle, der tager højde for overlappende contig'er og gap. ABACAS opretter en sammenligningsfil, som kan bruges til at visualisere ordnede og orienterede contig'er i ACT. Synteni er repræsenteret af røde bjælker, hvor farveintensiteten formindsker med lavere værdier procentidentitet mellem sammenlignelige blokke. Information om contig'er såsom orienteringen, procentidentitet, dækning og overlapning med andre contig'er kan også visualiseres ved at indlæse resultatfunktionsfil på ACT.
Translated by Michael Vogt
Located in Package: abacas
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This translation is managed by De danske oversættere af Ubuntu, assigned by Ubuntu Translators.

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