how to input paired end reads?

[Valentin-Bio]

Hello developer! I'm following your tutorial here https://github.com/sufforest/SolidBin

I'm on the step of generating coverage profiles and looking into the gen_cov.sh script I see the variable "read_dir" is used in minimap2 as the following:

for file in ${read_dir}/*; do echo $file; let cnt=cnt+1; echo $cnt; predix=basename ${file} minimap2 -t 30 -ax sr $assembly $file > ${mapdir}/${predix}.sam; done

This runs minimap2 considering the fastq files under ${reads_dir} are single end?

for running to paired end data I should run this ?

(assuming my paired end reads are forward = *_1.fastq.gz | reverse= *_2.fastq.gz)

for file in ${read_dir}/*_1.fastq.gz; do echo $file; base=$(basename $i "_1.fastq.gz") let cnt=cnt+1; echo $cnt; minimap2 -t 30 -ax sr $assembly ${base}_1.fastq.gz ${base}_2.fastq.gz > ${mapdir}/${base}.sam; done

if so , consider this a pull request ,

Best regards,

Valentín.

[Valentin-Bio]

I made my own sorted bam files from my fastq data files, is there a way in which I can generate a coverage profile file from these files?