Read Depths

Revision as of 10 August 2013 01:47 by admin (Comments | Contribs) | (→Hybrid error correction)

As described in the paper Hybrid error correction, second-generation data can be used to correct PacBio reads and then perform de novo assembly using PacBio corrected reads (PBcR). Here, we discuss the effects of depths on (1) hybrid error correction and (2) assembly.

Contents

Hybrid error correction

pacBioToCA -length 500 -partitions 200 -l PacBio_Illumia -s pacbio.spec

The file of pacbio.spec was downloaded from PacBioToCA and corrected to XXX.

Short read depth

We have used three short read depths (Raw, 118X and 100X) to correct long reads.

Long read depth

We have used subreads of 1-4 SMRT cells for different depths of long reads.

We arbitrary chose 1-4 SMRT cells:
Three single SMRT cell: m120208_071634, m120228_192221, m120228_210845
Two SMRT cells: m120228_210845 + m120208_122534
Three SMRT cells: m120228_115504 + m120228_152936 + m120228_100807
Four SMRT cells: m120228_171636 + m120228_223624 + m120228_100807 + m120228_190630

Performance

Name m120208_071634 m120228_192221 m120228_210845 Two SMRT cells Three SMRT cells Four SMRT cells
seqs amount:37077 seqs amount:38542 seqs amount:44794 seqs amount:77117 seqs amount:113284 seqs amount:136333
seq avg len:2023.338161 seq avg len:2322.679985 seq avg len:2334.414140 seq avg len:2184.208709 seq avg len:2333.977711 seq avg len:2386.664674
total:75.02 Mb total:89.52 Mb total:104.57 Mb total:168.44 Mb total:264.40 Mb total:325.38 Mb
depth: 16.13X depth: 19.25X depth: 22.49X depth: 36.22X depth: 56.86X depth: 69.97X
Corrected by raw data
seqs amount:26492 seqs amount:34981 seqs amount:40666 seqs amount:63760 seqs amount:98165 seqs amount:118901
seq avg len:2352.489884 seq avg len:2133.783826 seq avg len:2124.597010 seq avg len:2199.845561 seq avg len:2286.482249 seq avg len:2320.548322
total:62.32 Mb total:74.64 Mb total:86.40 Mb total:140.26 Mb total:224.45 Mb total:275.92 Mb
depth: 13.40X depth: 16.05X depth: 18.58X depth: 30.16X depth: 48.27X depth: 59.34X
Corrected by 118X
seqs amount:26666 seqs amount:64201 seqs amount:99285 seqs amount:120296
seq avg len:2309.110290 seq avg len:2150.165184 seq avg len:2221.782394 seq avg len:2252.656963
total:61.57 Mb total:138.04 Mb total:220.59 Mb total:270.99 Mb
depth: 13.24X depth: 29.69X depth: 47.44X depth: 58.28X
Corrected by 100X
seqs amount:25618 seqs amount:61415 seqs amount:95240 seqs amount:115080
seq avg len:2315.355024 seq avg len:2165.060164 seq avg len:2247.193879 seq avg len:2283.976060
total:59.31 Mb total:132.97 Mb total:214.02 Mb total:262.84 Mb
depth: 12.76X depth: 28.60X depth: 46.03X depth: 56.52X

Assembly

After read correction, PBcR can be used to de novo assemble the genome using runCA or Mira3.

We have assembled the genome with the all PBcR and the filtered PBcR (25X, using gatekeeper) by runCA, and evaluated the assemblies with QUAST 2.2.