assembling canu corrected reads about miniasm HOT 7 CLOSED

Could you check if the input contains duplicated read names?

from miniasm.

I don't think so the reads are in fasta format with read names in the format:

143b9016-9b2f-4a9f-b3e7-a87378b5afa2_Basecall_2D_2d NBCOL1105_Ecoli_644_3618_1_ch32_file16_strand

from miniasm.

Could you run the following and see if it gives any output?

zcat input.fa.gz | perl -ne 'print "$1\n" if />(\S+)/' | sort | uniq -d

from miniasm.

ok it has outputted the read names in order and there are no repeats

from miniasm.

That command line would have no output if there were no duplicated read names. -d means to output duplicated strings only.

from miniasm.

oh I see!! right I will sort out the file and try miniasm again, sorry!

from miniasm.

Never mind. I should have let minimap/miniasm check input name. This is actually a common error.

from miniasm.