From: Charles Plessy Date: Fri, 15 Oct 2021 03:45:30 +0000 (+0900) Subject: In GR X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=4c006c7a8b55ab0699a437f6239c62824baf96d3;p=source.git In GR --- diff --git a/biblio/10.1101_2020.03.14.992248v3.mdwn b/biblio/10.1101_2020.03.14.992248v3.mdwn deleted file mode 100644 index 5dc046eb..00000000 --- a/biblio/10.1101_2020.03.14.992248v3.mdwn +++ /dev/null @@ -1,13 +0,0 @@ -[[!meta title="HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads"]] -[[!tag bioRxiv genome assembly chromosome]] - -Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren - -bioRxiv 2020.03.14.992248; doi: https://doi.org/10.1101/2020.03.14.992248 - -HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads - -[[!doi 10.1101/2020.03.14.992248v3 desc="“HiCanu modifies the input reads by -compressing every homopolymer to a single nucleotide.” “Outputs contigs as -“pseudo-haplotypes” that preserve local allelic phasing but may switch between -haplotypes”"]] diff --git a/biblio/32801147.mdwn b/biblio/32801147.mdwn new file mode 100644 index 00000000..32b67e78 --- /dev/null +++ b/biblio/32801147.mdwn @@ -0,0 +1,13 @@ +[[!meta title="HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads"]] +[[!tag genome assembly chromosome]] + +Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren + +Genome Res. 2020 Sep;30(9):1291-1305. doi:10.1101/gr.263566.120 + +HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads + +[[!pmid 32801147 desc="“HiCanu modifies the input reads by +compressing every homopolymer to a single nucleotide.” “Outputs contigs as +“pseudo-haplotypes” that preserve local allelic phasing but may switch between +haplotypes”"]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 7c18baab..0ed2af28 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -23,6 +23,10 @@ fast. Shasta assemblies tend to be more fragmented, but have less disagreement with the reference. Shasta also comes with polishing modules similar to Racon and Medaka, but also to be faster. +The HiCanu assembler ([[Nurk, Walenz and coll., 2020|biblio/32801147]]) can +take advantage of high-accuracy sequences such as the ones of the PacBio HiFi +platform, to assemble multiple variants of the same locus. + Some genome assemblers produce a graph file that can be visualised with tools such as Bandage [[Wick and coll., 2015|biblio/26099265]].