SMRT Portal protocols - pb-dyim/SMRT-Analysis GitHub Wiki

Following are the secondary analysis protocols included in SMRT Analysis v1.4.0, with the SMRT Pipe module(s) called by each protocol.

RS_AHA_Scaffolding

• P_Filter
• HybridAssembly

RS_ALLORA_Assembly

• AlloraSFilter
• Assembly

RS_ALLORA_Assembly_EC

• AlloraSFIlter
• Assembly

RS_CeleraAssembler

• P_PacBioToCA
• P_CeleraAssembler

RS_Filter_Only

• P_Filter

RS_Minor_and_Compound_Variants

• P_Filter
• BLASR_Minor_and_Compound_Variants
• P_CorrelatedVariants

RS_Modification_Detection

• P_Filter
• P_Mapping
• P_GenomicConsensus
• P_Modification Detection

RS_Modification_and_Motif_Analysis

• P_Filter
• P_Mapping
• P_GenomicConsensus
• P_MotifFinder

RS_PreAssembler

• PreAssemblerSFilter
• P_PreAssembler

RS_PreAssembler_Allora

• PreAssemblerSFilter
• AlloraWithPreAssembler

RS_Resequencing

• P_Filter
• P_Mapping
• P_GenomicConsensus

RS_Resequencing_CCS

• P_Filter
• BLASR_De_Novo_CCS
• GenomicConcensus_Plurality

RS_Resequencing_CCS_GATK

• P_Filter
• BLASR_De_Novo_CCS
• P_GATKVC

RS_Resequencing_GATK

• P_Filter
• P_Mapping
• P_GATKVC

RS_Resequencing_GATK_Barcode

• P_Filter
• BLASR_Barcode
• P_GATKVC

RS_Site_Acceptance_Test

• P_Filter
• P_Mapping
• P_GenomicConsensus

RS_cDNA_Mapping

• P_Filter
• P_GMAP

11k_Unrolled_Resequencing

• P_Filter
• BLASR_Unrolled
• P_MotifFinder
• P_Modification Detection
• P_AnalysisHook

ecoliK12_RS_Resequencing

• P_Filter
• P_Mapping
• P_GenomicConsensus
• P_AnalysisHook

lambda_RS_Resequencing

• P_Filter
• P_Mapping
• P_GenomicConcensus
• P_AnalysisHook