freebayes vs longshot

[emilydolivo97]

Hello ,

I have 11 FASTQ files. These files were generated using nanopore technology. They belongs to fungis.
I have already used FreeBayes to detect variants. For this purpose, I utilized the following command for each FASTQ.gz file:

freebayes -f user/ref_genome/reference_sequence.fa -L SRAXXXX87.fastq.gz --vcf SRAXXX87.vcf --ploidy 2 --min-alternate-fraction 0.05

Now, I want to know what's the equivalent of this command using longshot. Does longshot generates snp, mnp, ins, del, or complex.
can longshot deals with multiple samples as it's the case for freebayes ? and does it generates phased haplotypes and genotypes please ?
Sorry for all these question but it's important for my studies and I'm stacked up

If it is, how do I use it please? which command and parameters to use exactly please ?

I hope that you could help me !!**