Café

diff --git a/biblio/10.1101_2020.03.16.993428.mdwn b/biblio/10.1101_2020.03.16.993428.mdwn
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+[[!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 6ff694351064c127364e954e1624d9d7bea77fb6..a07df442145827a88f506c137a6db41e25b74fb6 100644 (file)
--- 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