Contents [hide]

1 Dataset 5, E. coli K-12 MG1655, 17 SMRT cells 1.1 All Data 1.2 Randomly Selected Four SMRT cells 1.2.1 First Set 1.2.2 Second Set 1.2.3 Third Set 1.3 Randomly Selected Six SMRT cells 1.3.1 First Set 1.3.2 Second Set 1.3.3 Third Set 1.4 Randomly Selected eight SMRT cells 1.4.1 First Set 1.4.2 Second Set 1.4.3 Third Set 2 Dataset 6, E. coli K-12 MG1655, 8 SMRT cells 2.1 All Data 2.2 Randomly Selected Four SMRT cells 2.2.1 First Set 2.2.2 Second Set 2.2.3 Third Set 2.3 Randomly Selected Six SMRT cells 2.3.1 First Set 2.3.2 Second Set 2.3.3 Third Set 3 Dataset 7, M. ruber DSM1279, 4 SMRT cells 4 Dataset 8, P. heparinus DSM2366, 7 SMRT cells 4.1 All Data 4.2 Randomly Selected Four SMRT cell 4.2.1 First Set 4.2.2 Second Set 4.2.3 Third Set 5 Dataset 9, E. coli P4-C2 chemistry, 20Kbp library, 1 SMRT cells

Dataset 5, E. coli K-12 MG1655, 17 SMRT cells

All Data

The 17 SMRT cells of Ecoli MG 1655 were downloaded from NCBI SRA, as described in Data.
m120208_071634_42139_c100288480630000001523009507231245_s1_p0.bas.h5
m120228_190630_42139_c100301722550000001523012308061206_s1_p0.bas.h5
m120208_122534_42139_c100290260310000001523009507231262_s1_p0.bas.h5
m120228_192221_42129_c100298890010000001523009207231260_s1_p0.bas.h5
m120208_160812_42139_c100290260310000001523009507231264_s1_p0.bas.h5
m120228_205404_42139_c100301722550000001523012308061207_s1_p0.bas.h5
m120228_082105_42139_c100301722550000001523012308061200_s1_p0.bas.h5
m120228_210845_42129_c000304152550000001500000112311370_s1_p0.bas.h5
m120228_100807_42139_c100301722550000001523012308061201_s1_p0.bas.h5
m120228_223624_richard_c001202352550000001500000112311330_s1_p0.bas.h5
m120228_115504_42139_c100301722550000001523012308061202_s1_p0.bas.h5
m120229_004752_42129_c000304192550000001500000112311350_s1_p0.bas.h5
m120228_134222_42139_c100301722550000001523012308061203_s1_p0.bas.h5
m120229_012852_42139_c000301732550000001500000112311360_s1_p0.bas.h5
m120228_152936_42139_c100301722550000001523012308061204_s1_p0.bas.h5
m120229_193409_42129_c000304212550000001500000112311380_s1_p0.bas.h5
m120228_171636_42139_c100301722550000001523012308061205_s1_p0.bas.h5

We have run smrtpipe.py (SMRT analysis) with the following params.xml to get filtered subreads of continuous long reads (CLR).

 <param name="minLength">
   <value>50</value>
 </param>
 <param name="readScore">
   <value>0.75</value>
 </param>
 <param name="minSubReadLength">
   <value>50</value>

Randomly Selected Four SMRT cells

First Set

m120208_122534_42139_c100290260310000001523009507231262_s1_p0
m120228_205404_42139_c100301722550000001523012308061207_s1_p0
m120228_210845_42129_c000304152550000001500000112311370_s1_p0
m120228_152936_42139_c100301722550000001523012308061204_s1_p0

Filtered_four.fastq (Genome size: 4.65Mb)

seqs amount:142746

seq avg len:2286.987698

total:326.46 Mb

depth: 70.21X

Second Set

m120229_012852_42139_c000301732550000001500000112311360_s1_p0
m120228_152936_42139_c100301722550000001523012308061204_s1_p0
m120228_192221_42129_c100298890010000001523009207231260_s1_p0
m120228_100807_42139_c100301722550000001523012308061201_s1_p0

Filtered_four.fastq

seqs amount:157329

seq avg len:2274.563278

total:357.85 Mb

depth: 76.96X

Third Set

m120228_192221_42129_c100298890010000001523009207231260_s1_p0
m120228_223624_richard_c001202352550000001500000112311330_s1_p0
m120228_082105_42139_c100301722550000001523012308061200_s1_p0
m120229_193409_42129_c000304212550000001500000112311380_s1_p0

Filtered_four.fastq

seqs amount:146090

seq avg len:2309.804908

total:337.44 Mb

depth: 72.57X

Randomly Selected Six SMRT cells

First Set

m120228_190630_42139_c100301722550000001523012308061206_s1_p0
m120228_210845_42129_c000304152550000001500000112311370_s1_p0
m120228_205404_42139_c100301722550000001523012308061207_s1_p0
m120228_115504_42139_c100301722550000001523012308061202_s1_p0
m120229_012852_42139_c000301732550000001500000112311360_s1_p0
m120228_100807_42139_c100301722550000001523012308061201_s1_p0

Filtered_six.fastq (Genome size: 4.65Mb)

seqs amount:222213

seq avg len:2293.543920

total:509.66 Mb

depth: 109.60X

Second Set

m120208_071634_42139_c100288480630000001523009507231245_s1_p0
m120228_171636_42139_c100301722550000001523012308061205_s1_p0
m120208_160812_42139_c100290260310000001523009507231264_s1_p0
m120228_190630_42139_c100301722550000001523012308061206_s1_p0
m120208_122534_42139_c100290260310000001523009507231262_s1_p0
m120228_210845_42129_c000304152550000001500000112311370_s1_p0

Filtered_six.fastq

seqs amount:204851

seq avg len:2225.530273

total:455.90 Mb

depth: 98.04X

Third Set

m120228_223624_richard_c001202352550000001500000112311330_s1_p0
m120229_012852_42139_c000301732550000001500000112311360_s1_p0
m120228_082105_42139_c100301722550000001523012308061200_s1_p0
m120228_115504_42139_c100301722550000001523012308061202_s1_p0
m120228_190630_42139_c100301722550000001523012308061206_s1_p0
m120208_122534_42139_c100290260310000001523009507231262_s1_p0

Filtered_six.fastq

seqs amount:218732

seq avg len:2255.988808

total:493.46 Mb

depth: 106.12X

Randomly Selected eight SMRT cells

First Set

m120228_210845_42129_c000304152550000001500000112311370_s1_p0
m120208_122534_42139_c100290260310000001523009507231262_s1_p0
m120228_152936_42139_c100301722550000001523012308061204_s1_p0
m120228_223624_richard_c001202352550000001500000112311330_s1_p0
m120228_134222_42139_c100301722550000001523012308061203_s1_p0
m120208_160812_42139_c100290260310000001523009507231264_s1_p0
m120208_071634_42139_c100288480630000001523009507231245_s1_p0
m120228_192221_42129_c100298890010000001523009207231260_s1_p0

Filtered_eight.fastq (Genome size=4.65Mb)

seqs amount:276503

seq avg len:2270.814845

total:627.89 Mb

depth: 135.03X

Second Set

m120228_205404_42139_c100301722550000001523012308061207_s1_p0
m120229_193409_42129_c000304212550000001500000112311380_s1_p0
m120229_012852_42139_c000301732550000001500000112311360_s1_p0
m120228_171636_42139_c100301722550000001523012308061205_s1_p0
m120228_100807_42139_c100301722550000001523012308061201_s1_p0
m120229_004752_42129_c000304192550000001500000112311350_s1_p0
m120228_082105_42139_c100301722550000001523012308061200_s1_p0
m120208_160812_42139_c100290260310000001523009507231264_s1_p0

Filtered_eight.fastq

seqs amount:279608

seq avg len:2246.400929

total:628.11 Mb

depth: 135.08X

Third Set

m120208_160812_42139_c100290260310000001523009507231264_s1_p0
m120228_190630_42139_c100301722550000001523012308061206_s1_p0
m120228_205404_42139_c100301722550000001523012308061207_s1_p0
m120228_115504_42139_c100301722550000001523012308061202_s1_p0
m120229_004752_42129_c000304192550000001500000112311350_s1_p0
m120228_171636_42139_c100301722550000001523012308061205_s1_p0
m120229_012852_42139_c000301732550000001500000112311360_s1_p0
m120228_192221_42129_c100298890010000001523009207231260_s1_p0

Filtered_eight.fastq

seqs amount:270469

seq avg len:2285.672846

total:618.20 Mb

depth: 132.95X

Dataset 6, E. coli K-12 MG1655, 8 SMRT cells

All Data

The eight SMRT cells of Ecoli MG1655 were downloaded from HGAP. We used all SMRT cells and randomly selected four and six SMRT cells three times for each in our study.

m121023_202553_42178_c100389662550000001523034410251200_s1_p0.bas.h5
m121023_224605_42178_c100389662550000001523034410251201_s1_p0.bas.h5
m121024_010654_42178_c100389662550000001523034410251202_s1_p0.bas.h5
m121024_032737_42178_c100389662550000001523034410251203_s1_p0.bas.h5
m121024_074656_42178_c100389662550000001523034410251204_s1_p0.bas.h5
m121024_100442_42178_c100389662550000001523034410251205_s1_p0.bas.h5
m121024_122509_42178_c100389662550000001523034410251206_s1_p0.bas.h5
m121024_144608_42178_c100389662550000001523034410251207_s1_p0.bas.h5

We have run smrtpipe.py (SMRT analysis) with the following params.xml to get filtered subreads of continuous long reads (CLR).

 <param name="minLength">
   <value>50</value>
 </param>
 <param name="readScore">
   <value>0.75</value>
 </param>
 <param name="minSubReadLength">
   <value>50</value>

Filtered_four.fastq (Genome size: 4.65Mb)

seqs amount:187921

seq avg len:3190.512705

total:599.56 Mb

depth: 128.94X

Randomly Selected Four SMRT cells

First Set

m121024_100442_42178_c100389662550000001523034410251205_s1_p0
m121024_122509_42178_c100389662550000001523034410251206_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0

Filtered_four.fastq

seqs amount:96077

seq avg len:3187.676239

total:306.26 Mb

depth: 65.86X

Second Set

m121024_122509_42178_c100389662550000001523034410251206_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Filtered_four.fastq

seqs amount:98832

seq avg len:3171.085337

total:313.40 Mb

depth: 67.40X

Third Set

m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0
m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121024_074656_42178_c100389662550000001523034410251204_s1_p0

Filtered_four.fastq

seqs amount:88144

seq avg len:3228.205811

total:284.55 Mb

depth: 61.19.X

Randomly Selected Six SMRT cells

First Set

m121024_100442_42178_c100389662550000001523034410251205_s1_p0
m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_074656_42178_c100389662550000001523034410251204_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Filtered_six.fastq (Genome size: 4.65Mb)

seqs amount:1442277

seq avg len:3195.096439

total:454.59 Mb

depth: 97.76X

Second Set

m121024_074656_42178_c100389662550000001523034410251204_s1_p0
m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0
m121024_100442_42178_c100389662550000001523034410251205_s1_p0

Filtered_six.fastq

seqs amount:134536

seq avg len:2412.339453

total:428.75 Mb

depth: 92.20X

Third Set

m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_122509_42178_c100389662550000001523034410251206_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Filtered_six.fastq

seqs amount:144742

seq avg len:3198.577952

total:462.97 Mb

depth: 99.56X

Dataset 7, M. ruber DSM1279, 4 SMRT cells

Th four SMRT cells of Mruber were downloaded from HGAP.

m120803_022519_42141_c100388772550000001523034210251234_s1_p0.bas.h5
m120803_041200_42141_c100388772550000001523034210251235_s1_p0.bas.h5
m120803_055858_42141_c100388772550000001523034210251236_s1_p0.bas.h5
m120803_074648_42141_c100388772550000001523034210251237_s1_p0.bas.h5

We have run smrtpipe.py (SMRT analysis) with the following params.xml to get filtered subreads of continuous long reads (CLR).

 <param name="minLength">
   <value>50</value>
 </param>
 <param name="readScore">
   <value>0.75</value>
 </param>
 <param name="minSubReadLength">
   <value>50</value>

filtered_subreads.fastq (genome size: 3.1Mb)

seqs amount:156840

seq avg len:2444.683308

total:383.42 Mb

depth: 123.69X

Dataset 8, P. heparinus DSM2366, 7 SMRT cells

The seven SMRT cells of Phep were downloaded from HGAP. We used all SMRT cells and randomly selected four SMRT cells three times for each in our study.

All Data

m120802_210418_42142_c100388622550000001523034210251211_s1_p0.bas.h5
m120802_225401_42142_c100388622550000001523034210251212_s1_p0.bas.h5
m120803_004251_42142_c100388622550000001523034210251213_s1_p0.bas.h5
m120803_023226_42142_c100388622550000001523034210251214_s1_p0.bas.h5
m120803_041958_42142_c100388622550000001523034210251215_s1_p0.bas.h5
m120803_060809_42142_c100388622550000001523034210251216_s1_p0.bas.h5
m120803_075818_42142_c100388622550000001523034210251217_s1_p0.bas.h5

We have run smrtpipe.py (SMRT analysis) with the following params.xml to get filtered subreads of continuous long reads (CLR).

 <param name="minLength">
   <value>50</value>
 </param>
 <param name="readScore">
   <value>0.75</value>
 </param>
 <param name="minSubReadLength">
   <value>50</value>

Randomly Selected Four SMRT cell

First Set

m120802_225401_42142_c100388622550000001523034210251212_s1_p0
m120803_060809_42142_c100388622550000001523034210251216_s1_p0
m120803_004251_42142_c100388622550000001523034210251213_s1_p0
m120802_210418_42142_c100388622550000001523034210251211_s1_p0

Filtered_four.fastq (Genome size: 4.65Mb)

seqs amount:154190

seq avg len:2392.179623

total:368.85 Mb

depth: 71.34X

Second Set

m120803_023226_42142_c100388622550000001523034210251214_s1_p0
m120803_075818_42142_c100388622550000001523034210251217_s1_p0
m120802_210418_42142_c100388622550000001523034210251211_s1_p0
m120803_060809_42142_c100388622550000001523034210251216_s1_p0

Filtered_four.fastq

seqs amount:147932

seq avg len:2402.916198

total:355.47 Mb

depth: 68.76X

Third Set

m120803_041958_42142_c100388622550000001523034210251215_s1_p0
m120803_075818_42142_c100388622550000001523034210251217_s1_p0
m120803_023226_42142_c100388622550000001523034210251214_s1_p0
m120802_210418_42142_c100388622550000001523034210251211_s1_p0

Filtered_four.fastq

seqs amount:141326

seq avg len:2421.776170

total:342.26 Mb

depth: 66.20X

Dataset 9, E. coli P4-C2 chemistry, 20Kbp library, 1 SMRT cells

This dataset includes one SMRT Cell of data gathered with a PacBio RS II System and P4-C2 chemistry on a size selected 20kb library of E. coli K12. The data were downloaded from PacBio Devnet.

m130404_014004_sidney_c100506902550000001823076808221337_s1_p0.1.bax.h5
m130404_014004_sidney_c100506902550000001823076808221337_s1_p0.2.bax.h5
m130404_014004_sidney_c100506902550000001823076808221337_s1_p0.3.bax.h5

We have run smrtpipe.py (SMRT analysis) with the following params.xml to get filtered subreads of continuous long reads (CLR).

 <param name="minLength">
   <value>50</value>
 </param>
 <param name="readScore">
   <value>0.75</value>
 </param>
 <param name="minSubReadLength">
   <value>50</value>

filtered_subreads.fastq (genome size: 4.6Mb)

seqs amount:82590

seq avg len:5291.088292

total:436.99 Mb

depth: 94.19X