Main tool : polypolish
Full documentation: https://github.com/rrwick/Polypolish/wiki
Polypolish "polishes" consensus files created during assembly of long reads with Illumina short reads. Polypolish is a little different than other polishing tools in that paired-end reads need to be aligned separatly to generate two sam files.
Align reads to the draft sequence in a different container. The example shows bwa, as this is in the Polypolish wiki, but bbamp, minimap2 or any other similar software can perform a similar step that may be better suited for your use-case.
bwa index draft.fasta
bwa mem -t 16 -a draft.fasta reads_1.fastq.gz > alignments_1.sam
bwa mem -t 16 -a draft.fasta reads_2.fastq.gz > alignments_2.samOnce the sam files are generated, they can be used with polypolish in this container.
# paired end
polypolish filter --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam
polypolish polish draft.fasta filtered_1.sam filtered_2.sam > polished.fasta
# single end
polypolish polish draft.fasta input.sam > polished.fasta