SmrtPipe version |
1.87.139483 |
|
Job ID |
000221002 |
|
Input |
xml:input.xml |
|
Settings |
/net/eichler/vol4/home/jlhudd/projects/pacbio/cost_center/Filter_Only_P6.1.xml |
|
|
global.fetch |
common/protocols/preprocessing/Fetch.1.xml |
|
global.Control Filtering |
common/protocols/control/RemoveControlReads.1.xml |
|
global.version |
1 |
|
global.control |
/net/eichler/vol24/projects/sequencing/pacbio/nobackups/smrt_userdata/references/2kb_control |
|
global.name |
RS_Subreads |
|
global.barcode |
common/protocols/barcode/NoBarcode.1.xml |
|
global.description |
Filter subreads based on read length and quality, optionally splitting by barcode. Output FASTA and bas.h5 file of subreads. |
|
global.state |
active |
|
global.filtering |
common/protocols/filtering/SFilter.1.xml |
|
p_filter.minLength |
50 |
|
p_filter.moduleName |
P_Filter |
|
p_filter.minSubReadLength |
50 |
|
p_filterreports.moduleName |
P_FilterReports |
|
p_filter.description |
This module filters reads based on a minimum subread length, polymerase read quality and polymerase read length. |
|
p_filter.readScore |
75 |
|
p_fetch.description |
Sets up inputs |
|
p_fetch.moduleName |
P_Fetch |
|
p_filterreports.moduleName |
P_FilterReports |
|
p_controlreports.moduleName |
P_ControlReports |
|
p_control.pbalign_opts |
--algorithmOptions=" -maxScore -1000 -sdpTupleSize 8 " --minAccuracy 0.01 --minLength=50 --maxHits=1 |
|
p_controlreports.moduleName |
P_ControlReports |
|
p_control.moduleName |
P_Control |