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, minimap2, GSAlign and last), therefore providing different-species (lastz), same-species (blat and GSAlign) 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

Profiles

nf-LO comes with a series of pre-defined profiles:

• standard: this profile runs all dependencies in docker and other basic presets to facilitate the use
• local: runs using local exe instead of containerized/conda dependencies (see manual installation for further details)
• docker: force the use of docker
• singularity: runs the dependencies within singularity
• conda: runs the dependencies within conda
• uge: runs using UGE scheduling system
• sge: runs using SGE scheduling system A docker image is available with all the dependencies at tale88/nf-lo. This docker ships all necessary dependencies to run nf-LO. 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. GSAlign
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!

Input genomes

Source and target genomes can be either a local or remote (un)compressed fasta file. Source genome is the genome of origin, from which lift the positions. Target genome is the genome to which lift the position. We recommend to use soft-masked genomes to reduce computation time for aligners such as lastz. If the genome is unmasked, we provide nf-RM, a pipeline to perform repetitive element masking of genomes.

Running the pipeline

To test the pipeline locally, simply run:

nextflow run RenzoTale88/nf-LO 
    -profile test,docker

This will download and run the pipeline on the two toy genomes provided and generate liftover files. If you have all dependencies installed locally you can omit docker from the profile configuration.

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