From: Charles Plessy Date: Mon, 22 Nov 2021 09:08:35 +0000 (+0900) Subject: Kiwi X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=f1e21f60bf833c362c4ad8a3c6475f24211441f2;p=source.git Kiwi --- diff --git a/biblio/34320186.mdwn b/biblio/34320186.mdwn new file mode 100644 index 00000000..4a4d3a37 --- /dev/null +++ b/biblio/34320186.mdwn @@ -0,0 +1,10 @@ +[[!meta title="BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes."]] +[[!tag annotation software]] + +Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. + +Mol Biol Evol. 2021 Sep 27;38(10):4647-4654. doi:10.1093/molbev/msab199 + +BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. + +[[!pmid 34320186 desc="Based on OrthoDB v10. Uses MetaEuk by default on eukaryotes, but AUGUSTUS is still available."]] diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn index 0ed2af28..24b4f29f 100644 --- a/tags/assembly.mdwn +++ b/tags/assembly.mdwn @@ -80,12 +80,14 @@ interactive browsing with D-GENIES ([[Cabanettes and Klopp 2018|biblio/29888139]]). 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. 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]]. +2017|biblio/29220515]]) assesses the presence of evolutionary conserved +single-copy genes in the assemblies. Seppey, Manni and Zdobnov EM +([[2019|biblio/31020564]]) wrote a good introduction in _Methods Mol Biol_. +BUSCO v5 is based on OrthoDB v10, and support MetaEuk (default) and AUGUSTUS +for eukaryotes [[Manni and coll., 2021|biblio/34320186]]. + +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 Stancu and coll., 2017|biblio/29109544]]).