pbmm2 alignments Search Results


pbmm2  (Pacific Biosciences)
90
Pacific Biosciences pbmm2
Pbmm2, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/pbmm2/product/Pacific Biosciences
Average 90 stars, based on 1 article reviews
pbmm2 - by Bioz Stars, 2026-04
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structural variant caller pbsv  (Pacific Biosciences)
90
Pacific Biosciences structural variant caller pbsv
Three pipelines of the TransposonUltimate framework. ( A ) Given the nucleotide sequence of a transposon, relative k -mer frequencies (for k = 2, 3, 4) and binary protein features are extracted. These features are used by the random forest selective binary classifier (RFSB) to infer the transposon’s class. ( B ) Published transposon and protein annotation tools are applied to a given genome. Resulting annotations are filtered, merged and clustered using CD-HIT. Then, BLASTN is used to find additional full-length copies. ( C ) Sequencing reads obtained using a long-read technology from a probe genome are aligned onto a reference genome using ngmlr and <t>pbmm2.</t> Next, the alignments are used to discover structural variants. After filtering the structural variants, they are matched to the transposon annotations to detect transposition events.
Structural Variant Caller Pbsv, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/structural variant caller pbsv/product/Pacific Biosciences
Average 90 stars, based on 1 article reviews
structural variant caller pbsv - by Bioz Stars, 2026-04
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aligners sentieon-201808.07  (Sentieon Inc)
90
Sentieon Inc aligners sentieon-201808.07
Three pipelines of the TransposonUltimate framework. ( A ) Given the nucleotide sequence of a transposon, relative k -mer frequencies (for k = 2, 3, 4) and binary protein features are extracted. These features are used by the random forest selective binary classifier (RFSB) to infer the transposon’s class. ( B ) Published transposon and protein annotation tools are applied to a given genome. Resulting annotations are filtered, merged and clustered using CD-HIT. Then, BLASTN is used to find additional full-length copies. ( C ) Sequencing reads obtained using a long-read technology from a probe genome are aligned onto a reference genome using ngmlr and <t>pbmm2.</t> Next, the alignments are used to discover structural variants. After filtering the structural variants, they are matched to the transposon annotations to detect transposition events.
Aligners Sentieon 201808.07, supplied by Sentieon Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/aligners sentieon-201808.07/product/Sentieon Inc
Average 90 stars, based on 1 article reviews
aligners sentieon-201808.07 - by Bioz Stars, 2026-04
90/100 stars
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Image Search Results


Three pipelines of the TransposonUltimate framework. ( A ) Given the nucleotide sequence of a transposon, relative k -mer frequencies (for k = 2, 3, 4) and binary protein features are extracted. These features are used by the random forest selective binary classifier (RFSB) to infer the transposon’s class. ( B ) Published transposon and protein annotation tools are applied to a given genome. Resulting annotations are filtered, merged and clustered using CD-HIT. Then, BLASTN is used to find additional full-length copies. ( C ) Sequencing reads obtained using a long-read technology from a probe genome are aligned onto a reference genome using ngmlr and pbmm2. Next, the alignments are used to discover structural variants. After filtering the structural variants, they are matched to the transposon annotations to detect transposition events.

Journal: Nucleic Acids Research

Article Title: TransposonUltimate: software for transposon classification, annotation and detection

doi: 10.1093/nar/gkac136

Figure Lengend Snippet: Three pipelines of the TransposonUltimate framework. ( A ) Given the nucleotide sequence of a transposon, relative k -mer frequencies (for k = 2, 3, 4) and binary protein features are extracted. These features are used by the random forest selective binary classifier (RFSB) to infer the transposon’s class. ( B ) Published transposon and protein annotation tools are applied to a given genome. Resulting annotations are filtered, merged and clustered using CD-HIT. Then, BLASTN is used to find additional full-length copies. ( C ) Sequencing reads obtained using a long-read technology from a probe genome are aligned onto a reference genome using ngmlr and pbmm2. Next, the alignments are used to discover structural variants. After filtering the structural variants, they are matched to the transposon annotations to detect transposition events.

Article Snippet: We employ the structural variant caller Sniffles on ngmlr ( ) alignments and PBSV ( https://github.com/PacificBiosciences/pbsv ) structural variant caller on pbmm2 alignments of PacBio reads ( https://github.com/PacificBiosciences/pbmm2 ).

Techniques: Sequencing