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https://github.com/tobiasrausch/lorax
A long-read analysis toolbox for cancer and population genomics
https://github.com/tobiasrausch/lorax
amplicon bioinformatics cancer-genomics genomics long-read-sequencing long-reads telomere
Last synced: 2 months ago
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A long-read analysis toolbox for cancer and population genomics
- Host: GitHub
- URL: https://github.com/tobiasrausch/lorax
- Owner: tobiasrausch
- License: bsd-3-clause
- Created: 2022-01-20T09:14:36.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-03-18T10:26:44.000Z (9 months ago)
- Last Synced: 2024-03-18T11:52:20.080Z (9 months ago)
- Topics: amplicon, bioinformatics, cancer-genomics, genomics, long-read-sequencing, long-reads, telomere
- Language: C++
- Homepage:
- Size: 170 KB
- Stars: 18
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Authors: AUTHORS
Awesome Lists containing this project
README
[](http://bioconda.github.io/recipes/lorax/README.html)
[](https://anaconda.org/bioconda/lorax)
[](https://github.com/tobiasrausch/lorax/actions)
[](https://hub.docker.com/r/trausch/lorax/)
[](https://github.com/tobiasrausch/lorax/blob/master/LICENSE)
[](https://github.com/tobiasrausch/lorax/releases)
# Lorax: A long-read analysis toolbox for cancer and population genomics
In cancer genomics, long-read de novo assembly approaches may not be applicable because of tumor heterogeneity, normal cell contamination and aneuploid chromosomes. Generating sufficiently high coverage for each derivative, potentially sub-clonal, chromosome is not feasible. Lorax is a targeted approach to reveal complex cancer genomic structures such as telomere fusions, templated insertions or chromothripsis rearrangements. Lorax is NOT a long-read SV caller, this functionality is implemented in [delly](https://github.com/dellytools/delly).
## Installing lorax
Lorax is available as a [statically linked binary](https://github.com/tobiasrausch/lorax/releases/), a [singularity container (SIF file)](https://github.com/tobiasrausch/lorax/releases/) or as a [docker container](https://hub.docker.com/r/trausch/lorax/). You can also build lorax from source using a recursive clone and make. Lorax depends on [HTSlib](https://github.com/samtools/htslib) and [Boost](https://www.boost.org/).
`git clone --recursive https://github.com/tobiasrausch/lorax.git`
`cd lorax/`
`make all`
## Linear reference genomes
Lorax has several subcommands for alignments to linear reference genomes.
### Templated insertion threads
Templated insertions threads can be identified using
`lorax tithreads -g hg38.fa -o tithreads.bed -m control.bam tumor.bam`
The `out.bed` file specifies nodes (templated insertion source sequences) and edges (templated insertion adjacencies) of a graph that can be plotted using dot.
`cut -f 4,9 out.bed | sed -e '1s/^/graph {\n/' | sed -e '$a}' > out.dot`
`dot -Tpdf out.dot -o out.pdf`
The `out.reads` file lists unique assignments of reads to templated insertion source sequences. To extract the FASTA sequences for all these reads use the `lorax extract` subcommand (below) with the `-a` option.
`tail -n +2 out.reads | cut -f 1 | sort | uniq > reads.lst`
`lorax extract -a -g hg38.fa -r reads.lst tumor.bam`
### Telomere repeats associated with complex rearrangements
Telomere-associated SVs can be identified with lorax using
`lorax telomere -g t2t.fa -o outprefix tumor.bam`
The output files cluster reads into distinct telomere junctions that can be locally assembled. Since telomeres are repetitive, common mis-mapping artifacts found in a panel of normal samples are provided in the `maps` subdirectory. It is recommended to use the telomere-to-telomere assembly as the reference genome for `lorax telomere`.
### Read selection for targeted assembly of amplicons
Given a list of amplicon regions and a phased VCF file, lorax can be used to extract amplicon reads for targeted assembly approaches.
`lorax amplicon -g hg38.fa -s sample -v phased.bcf -b amplicons.bed tumor.bam`
The amplicon subcommand outputs the selected reads (as a hash list `out.reads`) and a diagnostic table (`out.bed`) with amplicon regions and their support by split-reads. Ideally, all amplicon regions are connected and belong to one connected component (one cluster of amplicons). This amplicon graph can be plotted using dot.
`cut -f 4,11 out.bed | sed -e '1s/^/graph {\n/' | sed -e '$a}' > out.dot`
`dot -Tpdf out.dot -o out.pdf`
To extract the FASTA sequences for all reads use the `lorax extract` subcommand (below) with the `-a` option.
### Extracting pairwise matches and FASTA sequences of reads
To get FASTA sequences and pairwise read to genome matches for a list of reads (`list.reads`) use
`lorax extract -g hg38.fa -r list.reads tumor.bam`
If the read list contains hashes instead of read names as from the `lorax amplicon` subcommand then please use the `-a` command-line option.
`lorax extract -a -g hg38.fa -r list.reads tumor.bam`
## Pan-genome graphs
For pan-genome graphs and pan-genome graph alignments, lorax supports the below subcommands, some are work-in-progress.
### Connected components of a pan-genome graph
`lorax components pangenome.gfa.gz > comp.tsv`
### Converting a pan-genome (sub-)graph to dot format
`lorax gfa2dot -s s103 -r 3 pangenome.gfa.gz > graph.dot`
`dot -Tpng graph.dot > graph.png`
### Converting pan-genome graph alignments to BAM
With long reads aligned to a pan-genome graph
`minigraph --vc -cx lr pangenome.gfa.gz input.fastq.gz | bgzip > sample.gaf.gz`
lorax can be used to convert the graph alignment to BAM
`lorax convert -g pangenome.gfa.gz -f input.fastq.gz sample.gaf.gz | samtools sort -o sample.bam -`
### Node coverage of pan-genome graph alignments
`lorax ncov -g pangenome.gfa.gz sample.gaf.gz > ncov.tsv`
## Citation
Tobias Rausch, Rene Snajder, Adrien Leger, Milena Simovic, Mădălina Giurgiu, Laura Villacorta, Anton G. Henssen, Stefan Fröhling, Oliver Stegle, Ewan Birney, Marc Jan Bonder, Aurelie Ernst, Jan O. Korbel
Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures
Cell Genomics, 2023, 100281, [DOI: 10.1016/j.xgen.2023.100281](https://doi.org/10.1016/j.xgen.2023.100281)
License
-------
Lorax is distributed under the BSD 3-Clause license. Consult the accompanying [LICENSE](https://github.com/tobiasrausch/lorax/blob/master/LICENSE) file for more details.