Input files

The software accepts inputs in the common fasta format, uncompressed or compressed with gzip. Input files can be specified as:

  1. Local files

  2. Remote links to a web file (e.g. ftp addresses)

  3. iGenomes accession

  4. NCBI RefSeq/Genbank accession (GCF or GCA codes)

Specify a local or remote source/target genome

To specify a local source or target genome, you can use the --source and --target flags followed by the path to the file:

nextflow run evotools/nf-LO --source /PATH/TO/source.fa --target /PATH/TO/target.fa

Similarly, you can download a remote file using the same command:

nextflow run evotools/nf-LO --source /PATH/TO/source.fa --target ftp://ncbi.nih.nlm.gov/PATH/TO/TARGET/genome.fa.gz

Download from iGenomes

Genomes can be downloaded from iGenome simply by adding the --igenome_source/igenome_target for the appropriate genome:

nextflow run evotools/nf-LO --source "danRer7" --target /PATH/TO/target.fa --igenome_source

Download from NCBI

nf-LO can download the genomes of interest from NCBI simply by adding the --ncbi_source/ncbi_target for the appropriate genome:

nextflow run evotools/nf-LO --source "danRer7" --target "GCA_001899175.1" --igenome_source --ncbi_target

nf-LO will use the dataset software to retrieve the genome of interest and then process it.

Conflicts

Remember that you can specify only 1 identifier for the source and 1 identifier for the target. If multiple source are provided for the source or the target, the pipeline will stop, not knowing which one to process. Therefore, remember to use:

  1. --source followed by the path/URL/NCBI accession/iGenomes name

  2. --target followed by the path/URL/NCBI accession/iGenomes name

  3. One of --ncbi_source or --igenome_source, if required

  4. One of --ncbi_target or --igenome_target, if required