```
docker run --rm quay.io/biocontainers/bwa:0.7.19--h577a1d6_1 bwa aln
```

Usage:   bwa aln [options] <prefix> <in.fq>

Options: -n NUM    max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
         -o INT    maximum number or fraction of gap opens [1]
         -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]
         -i INT    do not put an indel within INT bp towards the ends [5]
         -d INT    maximum occurrences for extending a long deletion [10]
         -l INT    seed length [32]
         -k INT    maximum differences in the seed [2]
         -m INT    maximum entries in the queue [2000000]
         -t INT    number of threads [1]
         -M INT    mismatch penalty [3]
         -O INT    gap open penalty [11]
         -E INT    gap extension penalty [4]
         -R INT    stop searching when there are >INT equally best hits [30]
         -q INT    quality threshold for read trimming down to 35bp [0]
         -f FILE   file to write output to instead of stdout
         -B INT    length of barcode
         -L        log-scaled gap penalty for long deletions
         -N        non-iterative mode: search for all n-difference hits (slooow)
         -I        the input is in the Illumina 1.3+ FASTQ-like format
         -b        the input read file is in the BAM format
         -0        use single-end reads only (effective with -b)
         -1        use the 1st read in a pair (effective with -b)
         -2        use the 2nd read in a pair (effective with -b)
         -Y        filter Casava-filtered sequences

