A lightweight wrapper to run minimap2 (v2.30) alignments directly on BAM file, powered by a robust Rust wrapper for minimap2 (minimap2-rs).
-
Efficiency: The
doradobinary is bloated for alignment-only use cases, imposing an unnecessary footprint. -
Flexibility: Limited access to
minimap2parameters indoradorestricts users' ability to fine-tune the alignment process. -
Ecosystem Integration (Conda Support):
doradolacks official support for Conda distribution, which hinders its integration into automated workflows and dependency management systems (likePixiorSnakemake).
conda install -c conda-forge -c bioconda bammap2Or:
conda install -c https://prefix.dev/waybio bammap2pixi global install bammap2Download from Github release
Usage: bammap2 [OPTIONS] <reference> <query>...
Arguments:
<reference> target.fa or target.idx
<query>... query sequences with BAM or fastq(.gz)/fasta(.gz), multiple files allowed. Use '-' for stdin. Stdin and pipe are only supported for BAM input and single file.
Options:
-h, --help Print help
-V, --version Print version
Indexing:
-k <INT> k-mer size (no larger than 28) [15]
-w <INT> minimizer window size [5]
-I <NUM> split index for every ~NUM input bases [16G] [default: 16G]
Mapping:
-f <FLOAT> filter out top FLOAT fraction of repetitive minimizers [0.0002]
-U <INT1,[INT2]> Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is max{INT1, min{INT2, -f}}. This option prevents excessively small or large -f estimated from the input reference.
-g <INT> stop chain enlongation if there are no minimizers in INT-bp [5000]
-G <INT> max intron length (effective with -xsplice; changing -r) [200k]
-F <INT> max fragment length (effective with -xsr or in the fragment mode) [800]
-r <INT,[INT]> chaining/alignment bandwidth and long-join bandwidth [500,20000]
-n <INT> minimal number of minimizers on a chain [3]
-m <INT> minimal chaining score (matching bases minus log gap penalty) [40]
-p <FLOAT> Min secondary-to-primary score ratio [0.8]
-N <INT> Retain at most N secondary alignments [5]
Alignments:
-A <INT> matching score [2]
-B <INT> mismatch penalty (larger value for lower divergence) [4]
-O <INT,[INT]> gap open penalty [4,24]
-E <INT,[INT]> gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [2,1]
-z <INT,[INT]> Z-drop score and inversion Z-drop score [400,200]
-s <INT> minimal peak DP alignment score [80]
Input/Output:
-o <FILE> output file path, currently only support output in BAM formst [stdout] [default: -]
-Y use soft clipping for supplementary alignments
--seed <INT> Integer seed for randomizing equally best hits. Minimap2 hashes INT and read name when choosing between equally best hits. [11] [default: 11]
--max-qlen <INT> skip reads longer than INT [0 (disabled)]
--secondary <secondary> Whether to output secondary alignments [default: yes] [possible values: yes, no]
-t <INT> number of threads [default: 8]
-K <STR> minibatch size for mapping [500M] [default: 500M]
Presets:
-x <STR> - lr:hq - accurate long reads (error rate <1%) against a reference genome
- splice/splice:hq - spliced alignment for long reads/accurate long reads
- asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5% sequence divergence
- sr - short reads against a reference
- map-pb/map-hifi/map-ont - CLR/HiFi/Nanopore vs reference mapping
- ava-pb/ava-ont - PacBio CLR/Nanopore read overlap
[default: lr:hq] [possible values: lr:hq, lr:hqae, map-hifi, map-pb, map-ont, asm5, asm10, asm20, sr, splice, splice:hq]Please cite the minimap2 papers.
Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. [doi:10.1093/bioinformatics/bty191][doi]
and/or:
Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2]
