Dear PenguiN team,
1. (Un)trusted-contigs option:
Have you considered adding an option to include existing contigs in the assembly process, alongside reads? Something like the (un)trusted-contigs option in SPAdes.
Could be useful for:
- Including contigs from previous assemblies
- Hybrid MG+MT datasets
- Iterative assembly refinement
2. Mixing paired and single-end reads:
This doesn't seem possible at the moment, but you are already trying to merge paired reads internally in paired-end mode using Flash, as far as I understand. What happens with the non-overlapping pairs?
Could I just merge/interleave them in a similar way as done by PenguiN prior to running, concatenate with the single-end reads, and then run?
This would be particularly useful for pipelines dealing with datasets that include both types of reads, allowing utilization of all available data in a single assembly run.
Best regards,
Oskar
Dear PenguiN team,
1. (Un)trusted-contigs option:
Have you considered adding an option to include existing contigs in the assembly process, alongside reads? Something like the (un)trusted-contigs option in SPAdes.
Could be useful for:
2. Mixing paired and single-end reads:
This doesn't seem possible at the moment, but you are already trying to merge paired reads internally in paired-end mode using Flash, as far as I understand. What happens with the non-overlapping pairs?
Could I just merge/interleave them in a similar way as done by PenguiN prior to running, concatenate with the single-end reads, and then run?
This would be particularly useful for pipelines dealing with datasets that include both types of reads, allowing utilization of all available data in a single assembly run.
Best regards,
Oskar