Input files for circlator
Circlator requires corrected reads and assembled contigs as input. It has been run successfully on the output of HGAP, PBcR and SPRAI. The location of the input files required by Circlator made by each assembler are listed below.
| Assembler | Corrected reads | Contigs |
|---|---|---|
| HGAP | data/corrected.fasta |
data/polished_assembly.fasta.gz |
| HGAP via SMRT Portal |
Preassembled Reads [1] |
Polished Assembly [1] |
| PBcR [2] | lib.fasta |
lib/9-terminator/asm.scf.fasta |
| SPRAI | c01.fin.idfq.gz |
CA/9-terminator/asm_CA_01_YYYYMMDD_HHMMSS.scf.fasta [3] |
[1] These files can be downloaded from the Assembly subsection of the Data panel of the left hand sidebar when viewing RS_HGAP_Assembly data in SMRT Portal. Both files should be downloaded in fasta format.
[2] Assuming that the option -l lib was used.
[3] The filename is different for each run of SPRAI. YYYYMMDD and HHMMSS must be replaced with the date and time.