From: Charles Date: Wed, 18 Dec 2019 05:06:45 +0000 (+0900) Subject: AUGUSTUS X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=9837611ff53a752f77946bfefb3b39dbf6424622;p=source%2F.git AUGUSTUS --- diff --git a/biblio/30466165.mdwn b/biblio/30466165.mdwn new file mode 100644 index 00000000..d4ca13ce --- /dev/null +++ b/biblio/30466165.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Predicting Genes in Single Genomes with AUGUSTUS."]] +[[!tag genome annotation software]] + +Hoff KJ, Stanke M. + +Curr Protoc Bioinformatics. 2019 Mar;65(1):e57. doi:10.1002/cpbi.57 + +Predicting Genes in Single Genomes with AUGUSTUS. + +[[!pmid 30466165 desc="Explain how to train AUGUSTUS for new species using transcriptome data."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 9f9bd5b6..0dbe7275 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -53,7 +53,11 @@ that most contact points are due to local (same-chromosome) proximity. Version BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll., 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy -genes in the assemblies. +genes in the assemblies. Seppey, Manni and Zdobnov EM ([[2019|biblio/31020564]]) +wrote a good introduction in _Methods Mol Biol_. + +BUSCO uses AUGUSTUS, and AUGUSTUS can be trained for a new species with +transcriptome data, as explained by [[Hoff and Stanke, 2018|biblio/30466165]]. A reference assembly can be used to search for structural variants in a different individual, for instance with NanoSV ([[Cretu and coll., 2017|biblio/29109544]]).