# Anchorwave 1.1.1


{{< admonition success "Installed" true >}}
This software should be available with no extra configuration.

This software is accessible with an alias. Typing the full path might be
required in some situations.
{{< /admonition >}}

## 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

{{< figure src="../images/anchorwave/workflow.png" alt="anchorwave workflow" >}}

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](https://github.com/smarco/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](https://github.com/baoxingsong/AnchorWave) for full
help and usage examples.

-------------------------------------------------------------------------------

## Location and version

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

## help message

```console
$ 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>