From 7ea34ce461f71244b697472a949c57bef9fcd953 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Wed, 8 May 2019 16:14:20 +0900 Subject: [PATCH] Flye published in Nat. Biotechnol. --- biblio/10.1101_247148.mdwn | 10 ---------- biblio/30936562.mdwn | 10 ++++++++++ tags/assembly.mdwn | 2 +- 3 files changed, 11 insertions(+), 11 deletions(-) delete mode 100644 biblio/10.1101_247148.mdwn create mode 100644 biblio/30936562.mdwn diff --git a/biblio/10.1101_247148.mdwn b/biblio/10.1101_247148.mdwn deleted file mode 100644 index 3b80d26d..00000000 --- a/biblio/10.1101_247148.mdwn +++ /dev/null @@ -1,10 +0,0 @@ -[[!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/biblio/30936562.mdwn b/biblio/30936562.mdwn new file mode 100644 index 00000000..77f9c76b --- /dev/null +++ b/biblio/30936562.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 + +Nat Biotechnol. 2019 May;37(5):540-546. doi:10.1038/s41587-019-0072-8 + +Assembly of Long Error-Prone Reads Using Repeat Graphs + +[[!pmid 30936562 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 e5d120f9..db55c0ff 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -9,7 +9,7 @@ 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 +2018|biblio/30936562]]) 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. (The predecessor of Flye, ABruijn, was reported by [[Istace and coll. -- 2.47.3