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Genome Annotation

LC Luis J. Chueca
JK Judith Kochmann
TS Tilman Schell
CG Carola Greve
AJ Axel Janke
MP Markus Pfenninger
SK Sven Klimpel
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(1) RepeatModeler v2.0: parameters: -pa 16 -LTRStruct; (2) RepeatMasker v4.1.0: parameters: -s -pa 18 -no_is -xsmall; (3) hisat v2.1.0: parameters: -k 3 –pen-noncansplice 12 -S; (4) GeMoMa v.1.7.1 [java v1.8.0_221]: 4.1 java -Xmx30G -jar GeMoMa-1.7.1.jar CLI ERE c=TRUE; 4.2 java -Xmx30G -jar GeMoMa-1.7.1.jar CLI DenoiseIntrons coverage_unstranded; 4.3 java -Xmx30G -jar GeMoMa-1.7.1.jar CLI GeMoMaPipeline tblastn=false r=EXTRACTED introns coverage_unstranded DenoiseIntrons.m=100000 GeMoMa.m=100000 GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true; 4.4 java -Xmx30G -jar GeMoMa-1.7.1.jar CLI GAF; 4.5 java -Xmx30G -jar GeMoMa-1.7.1.jar CLI AnnotationFinalizer u=YES i c=UNSTRANDED coverage_unstranded; 4.6 java -Xmx30G -jar GeMoMa-1.7.1.jar CLI Extractor p=true c=true; (5) BUSCO v3.0.2 [python v3.7.4 augustus v3.3.2]: parameters: -l /laurasiatheria_odb9/ -m prot; (6) Interproscan v5.39.77: parameters: -f tsv -iprlookup -pa -goterms -exclappl SignalP_GRAM_NEGATIVE,SignalP_GRAM_POSITIVE -dp; (7) ncbi-blast v.2.10.0: parameters: 7.1 makeblastdb -in uniprot_sprot_2020_04.fasta -parse_seqids -dbtype prot, 7.2 blastp -evalue 1e-6 -max_hsps 1 -max_target_seqs 1 -outfmt 6.

Copyright and License information:  ©2021 Chueca, Kochmann, Schell, Greve, Janke, Pfenninger and Klimpel.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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