Anchorwave 1.1.1

anchorwave-1.1.1

AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals.

By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy and merging them together, AnchorWave generates a whole-genome alignment for each collinear block. AnchorWave implements commands to guide collinear block identification with or without chromosomal rearrangements and provides options to use known polyploidy levels or whole-genome duplications to inform alignment.

Principle of the AnchorWave process

AnchorWave takes the reference genome sequence and gene annotation in GFF3 format as input and extracts reference full-length coding sequences (CDS) to use as anchors.

Using a splice aware alignment program (minimap2 and GMAP have been tested) to lift over the start and end position of reference full-length CDS to the query genome (step 1).

AnchorWave then identifies collinear anchors using one of three user-specified algorithm options (step 2) and uses the WFA algorithm to perform alignment for each anchor and inter anchor interval (step 4). Some anchor/inter-anchor regions cannot be aligned using our standard approach due to high memory and computational time costs. For these, AnchorWave either identifies novel anchors within long inter-anchor regions (step 3), or for those that cannot be split by novel anchors, aligns using the ksw_extd2 function implemented in minimap2 or a reimplemented sliding window approach (step 4). AnchorWave concatenates base pair sequence alignment for each anchor and inter-anchor region and outputs the alignment in MAF format (step 5).

Please see the readme for full help and usage examples.

Location and version

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$ which anchorwave
anchorwave=/local/cluster/anchorwave/bin/anchorwave
$ anchorwave --version
SSE4.1 is enabled
Program anchorwave v1.1.1

help message

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$ anchorwave --help
Program anchorwave v1.1.1
Usage: anchorwave <command> [options]
Commands:
    gff2seq     get the longest full-length CDS for each gene
    genoAli     whole chromosome global alignment and variant calling
    proali      genome alignment with relocation variation, chromosome fusion or whole genome duplication
    ali         perform global alignment for a pair of sequences using the 2-piece affine gap cost strategy

software ref: https://github.com/baoxingsong/AnchorWave
research ref: https://doi.org/10.1073/pnas.2113075119