From: Charles Date: Thu, 28 Feb 2019 04:18:56 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=c3262a728606113330a2f241a3a2057c16c3952b;p=source.git Café --- diff --git a/biblio/10.1101_247148.mdwn b/biblio/10.1101_247148.mdwn new file mode 100644 index 00000000..3b80d26d --- /dev/null +++ b/biblio/10.1101_247148.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Assembly of Long Error-Prone Reads Using Repeat Graphs"]] +[[!tag genome assembly method]] + +Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner + +bioRxiv, Posted January 12, 2018. + +Assembly of Long Error-Prone Reads Using Repeat Graphs + +[[!doi 10.1101/247148 desc="“Flye constructs (overlapping) contigs with possible assembly errors at the initial stage, combines them into an accurate assembly graph, resolves repeats in the assembly graph using small variations between various repeat instances that were left unresolved during the initial assembly stage, constructs a new, less tangled assembly graph based on resolved repeats, and finally outputs accurate contigs as paths in this graph.”"]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index c0b2a607..f1f20f03 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -8,6 +8,11 @@ Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows for the comparison of multiple Nanopore runs on the same plot, to assess if read length is satisfactory. +The Flye assembler ([[Kolmogorov and coll, bioRxiv +2018|biblio/10.1101_247148]]) creates an A-Bruijn (assembly) graph from draft +contigs using long error-prone reads, untangles the graph by resolving repeats, +and then uses it to refine the contings and increase their accuracy. + When coverage is too low for efficient reference-free assembly, related references can be used as a guide. The Ragout software ([[Kolmogorov and coll., 2014|biblio/24931998), [[Kolmogorov and coll., 2018|biblio/30341161]])