SMRT Subread Coverage & Assembly Parameter Estimator
Copyright © 2015 Richard J. Edwards - See source code for GNU License Notice
SMRTSCAPE (SMRT Subread Coverage & Assembly Parameter Estimator) is tool in development as part of our PacBio sequencing projects for predicting and/or assessing the quantity and quality of useable data required/produced for HGAP3 de novo whole genome assembly. The current documentation is below. Some tutorials will be developed in the future - in the meantime, please get in touch if you want to use it and anything isn't clear.
The main functions of
1. Estimate Genome Coverage and required numbers of SMRT cells given predicted read outputs. NOTE: Default settings for SMRT cell output are not reliable and you should speak to your sequencing provider for their up-to-date figures.
2. Summarise the amount of sequence data obtained from one or more SMRT cells, including unique coverage (one read per ZMW).
3. Calculate predicted coverage from subread data for difference length and quality cutoffs.
4. Predict HGAP3 length and quality settings to achieve a given coverage and accuracy.
NOTE: SMRTSCAPE Version 1 has been frozen at V1.10.1 (with the exception of bug fixes) and future development will be of SMRTSCAPE Version 2.x onwards. This is being reworked for FALCON assemblies.
Genome Coverage Options
SubRead Summary Options
Preassembly Fragmentation analysis Options
Assembly Parameter Options
History Module Version History
# 0.0.0 - Initial Compilation. # 1.0.0 - Initial working version for server. # 1.1.0 - Added xnlist=LIST : Additional columns giving % sites with coverage >= Xn [10,25,50,100]. # 1.2.0 - Added assessment -> now PAGSAT. # 1.3.0 - Added seed and anchor read coverage generator (calculate=T). # 1.3.1 - Deleted assessment function. (Now handled by PAGSAT.) # 1.4.0 - Added new coverage=T function that incorporates seed and anchor subreads. # 1.5.0 - Added parseparam=FILES with paramlist=LIST to parse restricted sets of parameters. # 1.6.0 - New SMRTSCAPE program building on PacBio v1.5.0. Added predict=T/F option. # 1.6.1 - Updated parameters=T to incorporate that the seed read counts as X=1. # 1.7.0 - Added *.summary.tdt output from subread summary analysis. Added minreadlen. # 1.8.0 - preassembly=FILE: Preassembly fasta file to assess/correct over-fragmentation (use seqin=FILE for subreads) # 1.9.0 - Updated empirical preassembly mapefficiency calculation. # 1.10.0 - Added batch processing of subread files. # 1.10.1 - Fixed bug in batch processing.
SMRTSCAPE_V1 REST Output formatsRun with
for more user-friendly formatted output. Individual outputs can be identified/parsed using
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.