Guide
Examples
Three assemblies are available from [http://code.google.com/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_Mauve How to score genome assemblies using the Mauve system]. == Sequence assembly == <table border=1> <tr> <td>'''''Assembly'''''</td><td>'''''Description'''''</td><td>'''''Download (*)'''''</td> </tr> <tr><td>[[Media:volc454|volc454.fa]]</td><td>It was sequenced using 454 pyrosequencing by Roach Inc on a GS FLX Titanium instrument. 25x coverage of reads were obtained. Reads were assembled to contigs with Newbler by Roache.</td><td>[[Media: assembly1.fasta|assembly1.fasta]]</td></tr> <tr><td>[[Media:volcV|volcV.fa]]</td><td>It was sequenced to 25x coverage using Illumina 100 nt read pairs with 500 nt inserts, and 15x coverage of 50 nt Illumina mate-pairs with 6.5 kbp insert. Both data type were generated by BGI. The assembly was constructed with velvet using the above ginve insert size estimates and default parameters. No read error ecoorection or quality trimming steps were performed.</td><td>[[Media: assembly2.fasta|assembly2.fasta]]</td></tr> <tr><td>[[Media:volcIDBA|volcIDBA.fa]]</td><td>It was sequenced with 80x coverage 76 nt read pairs with 300 nt inserts on an Illumina GAIIx instrument at UC Davis Genome Center, and 2x coverage of 50 nt mate-pairs with 6.5 kbp insert sequences at BGI. The reads were error corrected with REPTILE using default parameters, contigs assembled with IDBA using the custome parameters --mink 33 --maxk 78 and evertything else default, and scaffolded with SSPACE using the custom parameter -a 0.5 and everything else default.</td><td>[[Media:assembly3.fasta|assembly3.fasta]]</td></tr> </table> (*) The files only contain the contigs which were split at the >10 Ns. Merged File: [[Media:Mauve Contigs.fa|Mauve_contigs.fa]] {| border="1" cellspacing="0" cellpadding="5" align="left" Name!NumContigs!NumRefReplicons!NumAssemblyBases!NumReferenceBases!NumLCBs!DCJ_Distance!NumDCJBlocks!NumSNPs!NumMisCalled!NumUnCalled!NumGapsRef!NumGapsAssembly!TotalBasesMissed!PercBasesMissed!ExtraBases!PercExtraBases!MissingChromosomes!ExtraContigs!NumSharedBoundaries!NumInterLcbBoundaries!BrokenCDS!IntactCDS!ContigN50!ContigN90!MinContigLength!MaxContigLength - assembly1.fasta!157!5!3920004!4012900!13!121!121!90!90!0!141!128!119928!2.9886!1818!0.0464!0!44!1!8!30!3908!123582!11735!100!217295 - assembly2.fasta!1394!5!4394403!4012900!851!1652!1666!31356!925!30431!1848!1739!161388!4.0217!503214!11.4512!0!301!2!281!505!3433!843300!57!57!1354539 - assembly3.fasta!367!5!3880100!4012900!68!400!400!7093!1209!5884!999!991!155857!3.8839!22465!0.579!0!1!1!37!442!3496!19349!5537!234!99636 -
