dockstore-tool-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 -c input sequences are in the color space -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)

URL(s):

• https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcollaboratory%2Fdock...

View Associations