PacBio Corrected Reads (PBcR) Pipeline (original) (raw)

CA From Source Code

A version of source code is available (which correspond to that used in the publication). The code is compiled to support up to 64,786bp sequences for correction and assembly.

• Publication source (including CA, AMOS, SMRTportal, and utility scripts pre-built for Linux-amd64 machines) is available here
• List of commands used for correction and assembly is available here as well as in the distribution above.
• The latest code with updates and bug fixes can be built from the respository following the instructions here.
• For the latest usage information and announcements, please visit the PBcR wiki

Simulation Results

• An interactive KRONA chart of simulated assemblies given C1, C2, XL-C2, XL-XL, and ZL sequencing is available here.
• A list of repeat counts and maximum repeat size for all genomes is available here.
• The simulation results for # gaps remaining for a given coverage and chemistry type is available here

Datasets

Below you will find all the datasets used for testing the assembly/correction pipeline.
E. coli K12 PacBio RS sequences were generously provided by Pacific Biosciences.
Sequencing of E. coli O157, B. tre, M. haemolytica, and S. enterica were perfomed by the

1. E. coli K12 MG1655

• PacBio RS sequencing and 454 data are available at the SRA
• MiSeq Sequences are available at the Illumina scientific data website
• 200X Filtered fastq sequences direct link: fastq
• MiSeq 100X frg
• 454 50X frg
• CCS 25X frg

1. Ecoli O157:H7

• Raw sequences available at the SRA
• 200X Filtered fastq sequences direct link: fastq
• MiSeq 100X tar.gz
• 454 40X tar.gz

1. B. tre

• Raw sequences available at the SRA
• 200X Filtered fastq sequences direct link: fastq
• MiSeq 100X tar.gz
• 454 50X frg
• CCS 25X frg

1. M. hist

• Raw sequences available at the SRA
• 200X Filtered fastq sequences direct link: fastq
• MiSeq 100X tar.gz
• CCS 25X frg

1. F. tularensis

• Raw sequences available at the SRA
• All Filtered fastq sequences direct link: fastq
• 200X Filtered fastq sequences direct link: fastq
• MiSeq 100X tar.gz
• 454 50X frg

1. S. enterica

• Raw sequences available at the SRA
• 200X Filtered fastq sequences direct link: fastq
• MiSeq 56X tar.gz
• 454 25X tar.gz
• CCS 22X frg

Second-gen Assemblies

Below are the 454 and Illumina assemblies. 454 assemblies were generated by Newbler v2.8. Illumina assembles were generated by SPAdes v2.5.0 and MaSuRCA v1.9.5 and consensus-polished with iCORN.

1. Validation statistics on all generated assemblies in the paper is available here
2. E. coli K12

• MiSeq SPAdes assembly
• MiSeq SPAdes iCORN assembly
• MiSeq MaSuRCA assembly
• MiSeq MaSuRCA iCORN assembly
• 454 Newbler assembly

1. Ecoli O157

• MiSeq SPAdes assembly
• MiSeq SPAdes iCORN assembly
• MiSeq MaSuRCA assembly
• MiSeq MaSuRCA iCORN assembly
• 454 Newbler assembly

1. B. tre

• MiSeq SPAdes assembly
• MiSeq SPAdes iCORN assembly
• MiSeq MaSuRCA assembly
• MiSeq MaSuRCA iCORN assembly
• 454 Newbler assembly

1. M. haemolytica

• MiSeq SPAdes assembly
• MiSeq SPAdes iCORN assembly
• MiSeq MaSuRCA assembly
• MiSeq MaSuRCA iCORN assembly

1. F. tularensis

• MiSeq SPAdes assembly
• MiSeq SPAdes iCORN assembly
• MiSeq MaSuRCA assembly
• MiSeq MaSuRCA iCORN assembly
• 454 Newbler assembly

1. S. enterica

• MiSeq SPAdes assembly
• MiSeq SPAdes iCORN assembly
• MiSeq MaSuRCA assembly
• MiSeq MaSuRCA iCORN assembly
• 454 Newbler assembly

Corrected Sequences and Assembly

Below are the PBcR sequences and assemblies (both hybrid and second-gen alone). CA has some randomized code. Therefore, to reproduce the exact results in the paper, you must start with the corrected fastq sequences and assemble them rather than re-running correction and assembly.

1. Validation statistics on all generated assemblies in the paper is available here
2. E. coli K12

• PBcR Corrected sequences (via MiSeq)
• Assembly sequences (via MiSeq)
• PBcR Corrected sequences (via 454)
• Assembly sequences (via 454)
• PBcR Corrected sequences (via CCS)
• Assembly sequences (via CCS)
• PBcR Corrected sequences (via self-correction)
• Assembly sequences (via self-correction)

1. Ecoli O157

• PBcR Corrected sequences (via MiSeq)
• Assembly sequences (via MiSeq)
• PBcR Corrected sequences (via 454)
• Assembly sequences (via 454)
• PBcR Corrected sequences (via self-correction)
• Assembly sequences (via self-correction)

1. B. tre

• PBcR Corrected sequences (via MiSeq)
• Assembly sequences (via MiSeq)
• PBcR Corrected sequences (via 454)
• Assembly sequences (via 454)
• PBcR Corrected sequences (via CCS)
• Assembly sequences (via CCS)
• PBcR Corrected sequences (via self-correction)
• Assembly sequences (via self-correction)

1. M. haemolytica

• PBcR Corrected sequences (via MiSeq)
• Assembly sequences (via MiSeq)
• PBcR Corrected sequences (via CCS)
• Assembly sequences (via CCS)
• PBcR Corrected sequences (via self-correction)
• Assembly sequences (via self-correction)

1. F. tularensis

• PBcR Corrected sequences (via MiSeq)
• Assembly sequences (via MiSeq)
• PBcR Corrected sequences (via 454)
• Assembly sequences (via 454)
• PBcR Corrected sequences (via self-correction)
• Assembly sequences (via self-correction)
• PBcR All Data Corrected sequences (via self-correction)
• Assembly All Data sequences (via self-correction)

1. S. enterica

• PBcR Corrected sequences (via MiSeq)
• Assembly sequences (via MiSeq)
• PBcR Corrected sequences (via 454)
• Assembly sequences (via 454)
• PBcR Corrected sequences (via CCS)
• Assembly sequences (via CCS)
• PBcR Corrected sequences (via self-correction)
• Assembly sequences (via self-correction)