From: Charles Date: Wed, 27 Jan 2021 03:39:51 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=0e2d324db5caac977db1b229fbd3a3db454e3cd4;p=source.git Café --- diff --git a/biblio/10.1101_2020.03.16.993428.mdwn b/biblio/10.1101_2020.03.16.993428.mdwn new file mode 100644 index 00000000..f14b9cc5 --- /dev/null +++ b/biblio/10.1101_2020.03.16.993428.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms"]] +[[!tag bioRxiv assembly benchmark]] + +Nadège Guiglielmoni, Antoine Houtain, Alessandro Derzelle, Karine van Doninck, Jean-François Flot + +bioRxiv 2020.03.16.993428; doi: https://doi.org/10.1101/2020.03.16.993428 + +Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms + +[[!pmid 10.1101/2020.03.16.993428 desc="Benchark using a bdelloid rotifer. Performance of most software plateaus over 50× depth. purge_dups performed well on Flye assemblies. Filtering our shorter reads did not dramatically change the N50 of Flye 2.5 assemblies"]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 6ff69435..a07df442 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -53,6 +53,10 @@ Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an alternative to HaploMerger that takes read coverage into account when detecting potential haplotigs. However, it does not merge haplotypes. +`purge_dups`, another alternative tp HaploMerger and Purge Haplotivs, performed +well on Flye 2.5 assemblies ([[Guiglielmoni and coll.,2020 | +biblio/10.1101_2020.03.16.993428]]). + SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]]) takes Hi-C data and contigs as input and scaffolds them under the hypothesis that most contact points are due to local (same-chromosome) proximity. Version