Hello Daniel,
I’ve been checking the contigs length and they range from 300 to 2,000 bp, sometimes reaching up to 10,000 bp. Isn’t that considered long reads? In that case, should I use LAST or MALT?
I’d also like to ask you another thing (it may be pretty basic). My R1.fastq file contains 3,412,750 sequences (152 bp). After diamond blastx (against NCBI-nr) the number of queries aligned is 1,653,102. Doesn’t this represent a too low percentage of the total reads? This is the output from diamond blastx:
Reported 27513386 pairwise alignments, 27513529 HSPs.
1653102 queries aligned.