nf-LO

Nextflow LiftOver pipeline

Introduction

nf-LO is a nextflow implementation of the UCSC liftover pipeline. It comes with a series of presets, allowing alignments of genomes depending on their distance (near, medium and far). It also supports three different aligner (lastz, blat and minimap2), therefore providing different-species (lastz), same-species (blat) and ultra-fast liftovers from a source to a target genome.

Dependencies

Nextflow

Nextflow needs to be installed and in your path to be able to run the pipeline. To do so, follow the instructions here

Containers

A docker image is available with all the dependencies at tale88/nf-lo. This docker ships everything, with the exception of maf-convert, that needs to be installed separately and is necessary to run nf-LO with minimap2. Alernatively, a singularity build can be downloaded with the following. This is the recommended mode of usage of the software, since all the dependencies come shipped in the container.

Manual installation

In the case the system doesn't support docker/singularity, it is possible to download them all through the script install.sh. This script will download a series of software and save them in the ./bin folder, including:

1. lastz
2. blat
3. minimap2
4. last
5. nucmer
6. Many exe from the kent toolkit:
   • axtChain
   • chainAntiRepeat
   • chainMergeSort
   • chainNet
   • chainPreNet
   • chainStitchId
   • chainSplit
   • faSplit
   • faToTwoBit
   • liftOver
   • liftUp
   • netChainSubset
   • netSyntenic
   • twoBitInfo
   • lavToPsl Remember to add the bin folder to your path with the command:

export PATH=$PATH:$PWD/bin

Or link te folder to the working directory:

ln -s /PATH/TO/bin

Ready to go!

Running the pipeline

To run the pipeline locally, simply copy main.nf in the folder where you want to run the analysis. To run the example, first download the data:

mkdir test && cd test
wget https://sra-download.ncbi.nlm.nih.gov/traces/wgs03/wgs_aux/JZ/EF/JZEF01/JZEF01.1.fsa_nt.gz && gunzip JZEF01.1.fsa_nt.gz
wget https://sra-download.ncbi.nlm.nih.gov/traces/wgs03/wgs_aux/JZ/EG/JZEG01/JZEG01.1.fsa_nt.gz && gunzip JZEG01.1.fsa_nt.gz

Then, copy main.nf in the folder and run the pipeline:

nextflow run main.nf \
    --source $PWD/test/JZEF01.1.fsa_nt \
    --target $PWD/test/JZEG01.1.fsa_nt \
    --outdir $PWD/test/OUTPUT_NEW \
    --distance medium \
    --aligner minimap2 \
    --tgtSize 1000000 \
    --srcSize 500000 \
    --srcOvlp 100000 

This will run the pipeline on the two toy genomes provided and return a liftover. It will perform the analysis chunking the target in 1Mb windows, and the source in 500Kb, with 100Kb extra bytes as overlaps (600Kb long in total). The aligner will be minimap2 and the distance set to medium (asm10). The whole process should take few minutes to complete. Using other aligners will likely increase the run time, but should still be reasonably low.

If you want to run the pipeline using the docker container, you can add -with-docker tale88/nf-lo at the end of your command line, and this should run the pipeline downloading the docker container specified inclusive of all the dependencies.

If instead, you prefer using a singularity image, you can run it through -with-singularity library://renzo_tale/default/nf-lo

References

Adaptive seeds tame genomic sequence comparison. Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Genome Res. 2011 21(3):487-93; http://dx.doi.org/10.1101/gr.113985.110 Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. http://dx.doi.org/10.1093/bioinformatics/bty191 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64