Can PALACE take pre-assembled contigs generated by Megahit and fastq files processed by fastp as input, to avoid redundant computation and save runtime?

[1023011930]

Thank you for developing this pioneering software. I would like to inquire whether PALACE only accepts paired-end FASTQ files as input. Would it be feasible for you to add support for pre-assembled contigs together with quality-trimmed FASTQ reads as inputs, which could greatly reduce computational time costs?

[panguangze]

Currently, PALACE only accepts paired-end FASTQ files as input. However, we plan to support this new input mode in future updates, along with integration for mainstream assembly software. Although we have not tested this specific scenario, if you have MetaSPAdes assembly results, there is a potential workaround: place your assembly files in the $out_dir/02-assembly directory, and create softlinks (symbolic links) to your quality‑trimmed FASTQ reads as $out_dir/01-qc/${prefix}_1_filter.fastq and $out_dir/01-qc/${prefix}_2_filter.fastq. This approach may allow the pipeline to run successfully.

[1023011930]

Thank you for your reply.
I would like to follow up with a question: would it be acceptable to also place the Megahit contig files in the $out_dir/02-assembly directory? This would save a considerable amount of time. If you think this is feasible, I will go ahead and try this setup.
Thank you.

[panguangze]

Thank you for your reply. I would like to follow up with a question: would it be acceptable to also place the Megahit contig files in the $out_dir/02-assembly directory? This would save a considerable amount of time. If you think this is feasible, I will go ahead and try this setup. Thank you.

Sorry, Megahit results are not available at this time. We plan to include support for Megahit in future updates.