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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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polishing Smartdenovo assembly #37

Closed biowackysci closed 5 years ago

biowackysci commented 5 years ago

Hello, I have a couple of questions. 1) I was thinking of using Racon to polish the smartdenovo assembly. Racon suggests to use these reads: racon [options ...] 

<sequences>
    input file in FASTA/FASTQ format (can be compressed with gzip)
    containing sequences used for correction
<overlaps>
    input file in MHAP/PAF/SAM format (can be compressed with gzip)
    containing overlaps between sequences and target sequences
<target sequences>
    input file in FASTA/FASTQ format (can be compressed with gzip)
    containing sequences which will be corrected

for the first sequences, I can give illumina reads as the input , I am not sure what would be the best input for the second sequnces as smartdenovo does not make any mhap files like other assemblers like Canu and for the third sequences I will input the .cns file generated by smartdenovo assembly.

Can you please help me out what needs to go in the input files for the overlaps? 2) is there a better polishing tool other than Racon for Smartdenovo assembly? Note : I have used long reads from both PacBio and Nanopore for my assembly

Thanks heaps in advance S

ruanjue commented 5 years ago

I am not sure how to run Racon, but from your description, PAF and SAM file can be generated by minimap2. I used to polish the contigs with Quiver and pilon.

Best, Jue