H. volc

Revision as of 24 December 2011 01:35 by admin (Comments | Contribs) | (→Sequence assembly)

Haloferax volcanii DS2

Contigs source

Three assemblies are available from How to score genome assemblies using the Mauve system.


Sequence assembly

Assembly Description Download §
volc454 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. assembly1.fasta
volcV 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. assembly2.fasta
volcIDBA 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. assembly3.fasta

§The files only contain the contigs, where scaffolds were split whenever >10 Ns occurs.

Merged File: Mauve_Contigs.fa

  • Scored with Mauve metrics:
Name NumContigs NumAssemblyBases NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed PercBasesMissed ExtraBases PercExtraBases BrokenCDS IntactCDS ContigN50 ContigN90 MaxContigLength
volc454 157 3920004 90 0 141 128 119928 2.9886 1818 0.0464 30 3908 123582 11735 217295
volcV 1394 4394403 925 30431 1848 1739 161388 4.0217 503214 11.4512 505 3433 843300 57 1354539
volcIDBA 367 3880100 1209 5884 999 991 155857 3.8839 22465 0.579 442 3496 19349 5537 99636

Contig integrator

Integrator Download
CISA CISA
minimus2 minimus2


Evaluation

  • Benchmark genome
Haloferax_volcanii_DS2.gbk
  • Evaluate by Mauve Assembly Metrics
How to score genome assemblies using the Mauve system
  • Score with Mauve metrics:
Name NumContigs NumAssemblyBases NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed PercBasesMissed ExtraBases PercExtraBases BrokenCDS IntactCDS ContigN50 ContigN90 MaxContigLength
assembly1 157 3920004 90 0 141 128 119928 2.9886 1818 0.0464 30 3908 123582 11735 217295
assembly2 1555 3855484 762 1527 1541 1542 197907 4.9318 16765 0.4348 450 3488 9037 1862 55518
assembly3 580 3871717 988 548 1080 989 162341 4.0455 20132 0.52 438 3500 12787 3473 53121
CISA 115 4065722 368 21 179 153 178464 4.4473 122419 3.011 51 3887 116113 16493 206444
minimus2 69 3950442 1097 0 325 84 80997 2.0184 15785 0.3996 206 3732 169764 25881 427810