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loneknightpy / idba

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Single reads as input possible? #66

Open Krannich479 opened 2 years ago

Krannich479 commented 2 years ago

Hi, I am attempting to assemble PE short-read data (2x150bp, FASTQ). However, I have some single reads too due to unaligned mates. I understand that a first step is to convert my pair1.fq and pair2.fq into an interleaved reads.fa (i.e. reads in a pair are consecutive in the FASTA). But is there a possibility to include the single reads too? I am looking for something comparable to SPAdes' or Minia's -s option.

Any help/info appreciated. Thanks!

jvollme commented 2 years ago

I guess you could use the -l ("long_reads") option? But just out of curiosity...this assembler seems to be without updates/support since about 5 years. Why do you want to use it instead of e.g. Spades or Megahit(which at least don't require that cumbersome fastq to fasta conversion)?