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Maggi-Chen / Inspector

A tool for evaluating long-read de novo assembly results
MIT License
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Inspector seems doesn't fix the small-scale errors #19

Closed hq66 closed 1 year ago

hq66 commented 1 year ago

Hi~ I used the command "inspector.py -c ctg.fa -r ccs1.fq ccs2.fq -o inspector_out/ --datatype hifi" to evaluate the ctg-level draft assembly. But I found the output "valid_contig.fa" was exactly the same as the input "ctg.fa". I careflly compared the size of contigs and the base sequence in "small_scale_error.bed", and I'm sure the "valid_contig.fa" makes no difference. The "summary_statistics" did output errors, but I wonder why they were not fixed in "valid_contig.fa".

Maggi-Chen commented 1 year ago

Hello,

The script 'inspector.py' only evaluates the assembly and identifies assembly errors. The 'valid_contig.fa' includes original uncorrected contigs. Error correction is done by running additional step of "inspector-correct.py -i inspector_out/ --datatype pacbio-hifi ". You will find corrected assembly in a file named 'corrected_contig.fa'.

Best, Maggi

hq66 commented 1 year ago

Hello,

The script 'inspector.py' only evaluates the assembly and identifies assembly errors. The 'valid_contig.fa' includes original uncorrected contigs. Error correction is done by running additional step of "inspector-correct.py -i inspector_out/ --datatype pacbio-hifi ". You will find corrected assembly in a file named 'corrected_contig.fa'.

Best, Maggi

Thanks for your reply!