Hi inspector Team,
I used the inspector to perform assembly correction of two haplotype-resolved HiFi assemblies of a human individual. I can see the assembly QV is better, but one of assemblies shows more structural errors after correction. In addition, I also found the local assembly would fail in inspector correction. Is it possible for me to address these issues? Thanks!
Hi inspector Team, I used the inspector to perform assembly correction of two haplotype-resolved HiFi assemblies of a human individual. I can see the assembly QV is better, but one of assemblies shows more structural errors after correction. In addition, I also found the local assembly would fail in inspector correction. Is it possible for me to address these issues? Thanks!
commands: inspector.py -c asm1.fa -r ccsreads.1.fastq ccsreads.2.fastq -o asm1_out/ --datatype hifi inspector.py -c asm2.fa -r ccsreads.1.fastq ccsreads.2.fastq -o asm2_out/ --datatype hifi
inspector-correct.py -i asm1_out/ --datatype pacbio-hifi -o asm1_corrected/ inspector-correct.py -i asm2_out/ --datatype pacbio-hifi -o asm2_corrected/
asm2 before correction: Structural error 49 Expansion 29 Collapse 20 Haplotype switch 0 Inversion 0
Small-scale assembly error /per Mbp 14.790265745042309 Total small-scale assembly error 44683 Base substitution 26180 Small-scale expansion 10097 Small-scale collapse 8406
QV 46.40314095738277
asm2 after correction: Structural error 58 Expansion 32 Collapse 26 Haplotype switch 0 Inversion 0
Small-scale assembly error /per Mbp 1.3369275599703823 Total small-scale assembly error 4039 Base substitution 3227 Small-scale expansion 349 Small-scale collapse 463
QV 50.03862621625856