Alternative Aligners

[alexg9010]

Collecting new aligners to integrate into the pipeline

Here we are starting a collection of more recent aligners/wrappers that could be implemented as additional/alternative aligners for the pigx-bsseq pipeline.

The aligners collected here have to support bisulfite converted reads.

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Please follow this template to add information about a new item:

## New-BS-Mapper-X

### Improvements

A small section about benefits of the new aligner: This is a recent aligner based on X and provides a decent speed-up compared to Bismark/bowtie2. 

### Performance Comparison

Put Figure 
![Performance Comparison](https://genome.cshlp.org/content/31/7/1290/T2.large.jpg)

Or Table here 

Depth|	Bwa-meth|	Novo align|	Bismark|	GEM3|	Bis-SNP|	Methyl Extract|	BScall
27× | 278.7 | 2419.6 | 354.3 | 33.5 | 266.8 | 204.9 | 6.2
58× | 612.5 | 5050.9 | 732.6 | 69.2 | 419.5 | 372.5 | 8


### Details

Commands to run are described here: <put link here>

The output format is described here: <put link here>

### Open Questions 

* [ ] check how this compares against bismark
* [ ] check how this compares against bwa-meth

### Resources

paper: <put link here>
docs: <put link here>
code: <put link here>

[alexg9010]

HISAT-3N

Improvements

This is a recent aligner based on HISAT2 and provides decent speed-up compared to bismark/bowtie2.

Performance Comparison

Details

Commands to run are described here: https://github.com/DaehwanKimLab/hisat2/tree/hisat-3n#examples-3

The output format is described here: https://github.com/DaehwanKimLab/hisat2/tree/hisat-3n#sample-3n-conversion-table

Open Questions

• check how this compares against bwa-meth
• check if the results are comparable to bismark output

Resources

paper: https://genome.cshlp.org/content/31/7/1290.full
docs: https://daehwankimlab.github.io/hisat2/hisat-3n/
code: https://github.com/DaehwanKimLab/hisat2/tree/hisat-3n

[alexg9010]

gemBS

Improvements

GEMBS is a bioinformatic pipeline designed for high-throughput analysis of DNA methylation from whole genome bisulfites sequencing data (WGBS). It employs GEM3, a high performance read aligner and BScall, a variant caller specifically for bisulfite sequencing data.

GEMBS produces alignment BAM files, BCF files with variant calls and methylation values, BED files with methylation at CpG and non-CpG sites, bigBed and BigWig files for visualisation of methylation data in a genome browser along with comprehensive QC reports on the mapping and calling process.

Performance Comparison

Details

Commands to run are described here: http://statgen.cnag.cat/gemBS/UserGuide/_build/html/example.html

The output format is described here: http://statgen.cnag.cat/gemBS/UserGuide/_build/html/pipelineExtract.html

Open Questions

• [ x] check how this compares against bismark
• [ x] check how this compares against bwa-meth

Resources

paper: https://academic.oup.com/bioinformatics/article/35/5/737/5077236
docs: http://statgen.cnag.cat/GEMBS/index.html
code: gemBS V3 | gemBS V4