On examination of the read length distribution of QC reads, I found that 15-20% of the total QC reads are below 60 bp (5% are of 0-10bp) and I would not consider them for either taxonomic classification or assembly.
In that case, Is there any functionality in KneadData that discards the read if it falls below specific read length?
Following up on this, I found that sequence of parameters provided to trimmomatic are important and does trick for me:
Following code did not discard reads below 60bp:-
–trimmomatic-options=“ILLUMINACLIP:/NexteraPE-PE.fa:2:30:10” --trimmomatic-options=“MINLEN:60” --trimmomatic options=“SLIDINGWINDOW:5:25”
However, following code did discard reads below 60bp:-
–trimmomatic-options=“ILLUMINACLIP:/NexteraPE-PE.fa:2:30:10” --trimmomatic options=“SLIDINGWINDOW:5:25” --trimmomatic-options=“MINLEN:60”
But please let me know if there is anything I completely missed in this.