Setting contig size limit in metaSpades

usegalaxy.org.au support
1

Hi, I am running metaSpades, and would like to set a minimum contig length for the assembly (2000 nt). However, I do not see an option for this setting. Are you able to help? Thanks.

2

Would it be an option for you to use fastp or cutadapt to remove the short contigs afterwards? You may need to double check the default values of those tools so you only do the length filtering and no other trimming.

3

Hi @ranitori
Maybe filter the contigs using Filter sequences by length (available in FASTA/FASTQ section).
Kind regards,
Igor

4

Thanks @gbbio and @igor for the suggestions, much appreciated.