{"id":6242,"projects":[69],"description":"Usage:   bwa aln [options] <prefix> <in.fq>\n\nOptions: -n NUM    max #diff (int) or missing prob under 0.02 err rate (float) [0.04]\n         -o INT    maximum number or fraction of gap opens [1]\n         -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]\n         -i INT    do not put an indel within INT bp towards the ends [5]\n         -d INT    maximum occurrences for extending a long deletion [10]\n         -l INT    seed length [32]\n         -k INT    maximum differences in the seed [2]\n         -m INT    maximum entries in the queue [2000000]\n         -t INT    number of threads [1]\n         -M INT    mismatch penalty [3]\n         -O INT    gap open penalty [11]\n         -E INT    gap extension penalty [4]\n         -R INT    stop searching when there are >INT equally best hits [30]\n         -q INT    quality threshold for read trimming down to 35bp [0]\n         -f FILE   file to write output to instead of stdout\n         -B INT    length of barcode\n         -c        input sequences are in the color space\n         -L        log-scaled gap penalty for long deletions\n         -N        non-iterative mode: search for all n-difference hits (slooow)\n         -I        the input is in the Illumina 1.3+ FASTQ-like format\n         -b        the input read file is in the BAM format\n         -0        use single-end reads only (effective with -b)\n         -1        use the 1st read in a pair (effective with -b)\n         -2        use the 2nd read in a pair (effective with -b)","image":"","tags":"","type":"","title":"dockstore-tool-bwa-aln","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcollaboratory%2Fdockstore-tool-bwa-aln","authors":[1],"rubrics":[25]}