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An accurate homology lift-over tool between assemblies
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v1.0.0
usage: lifton [-h] [-E] [-EL] [-c] [-o FILE] [-u FILE] [-exclude_partial] [-mm2_options =STR] [-a A] [-s S] [-min_miniprot MIN_MINIPROT]
[-max_miniprot MAX_MINIPROT] [-d D] [-flank F] [-V] [-D] [-t THREADS] [-m PATH] [-f TYPES] [-infer-genes] [-infer_transcripts] [-chroms TXT]
[-unplaced TXT] [-copies] [-sc SC] [-overlap O] [-mismatch M] [-gap_open GO] [-gap_extend GE] [-polish] [-cds] -g GFF [-P FASTA] [-T FASTA] [-L gff]
[-M gff] [-ad SOURCE]
target reference
Lift features from one genome assembly to another
* Required input (sequences):
target target fasta genome to lift genes to
reference reference fasta genome to lift genes from
* Required input (Reference annotation):
-g GFF, --reference-annotation GFF
the reference annotation file to lift over in GFF or GTF format (or) name of feature database; if not specified, the -g argument must be
provided and a database will be built automatically
* Optional input (Reference sequences):
-P FASTA, --proteins FASTA
the reference protein sequences.
-T FASTA, --transcripts FASTA
the reference transcript sequences.
* Optional input (Liftoff annotation):
-L gff, --liftoff gff
the annotation generated by Liftoff (or) name of Liftoff gffutils database; if not specified, the -liftoff argument must be provided and a
database will be built automatically
* Optional input (miniprot annotation):
-M gff, --miniprot gff
the annotation generated by miniprot (or) name of miniprot gffutils database; if not specified, the -miniprot argument must be provided
and a database will be built automatically
* Output settings:
-o FILE, --output FILE
write output to FILE in same format as input; by default, output is written to "lifton.gff3"
-u FILE write unmapped features to FILE; default is "unmapped_features.txt"
-exclude_partial write partial mappings below -s and -a threshold to unmapped_features.txt; if true partial/low sequence identity mappings will be included
in the gff file with partial_mapping=True, low_identity=True in comments
* Miscellaneous settings:
-h, --help show this help message and exit
-E, --evaluation Run LiftOn in evaluation mode
-EL, --evaluation-liftoff-chm13
Run LiftOn in evaluation mode
-c, --write_chains Write chaining files
-V, --version show program version
-D, --debug Run debug mode
-t THREADS, --threads THREADS
use t parallel processes to accelerate alignment; by default p=1
-m PATH Minimap2 path
-f TYPES, --features TYPES
list of feature types to lift over
-infer-genes use if annotation file only includes transcripts, exon/CDS features
-infer_transcripts use if annotation file only includes exon/CDS features and does not include transcripts/mRNA
-chroms TXT comma seperated file with corresponding chromosomes in the reference,target sequences
-unplaced TXT text file with name(s) of unplaced sequences to map genes from after genes from chromosomes in chroms.txt are mapped; default is
"unplaced_seq_names.txt"
-copies look for extra gene copies in the target genome
-sc SC with -copies, minimum sequence identity in exons/CDS for which a gene is considered a copy; must be greater than -s; default is 1.0
-overlap O maximum fraction [0.0-1.0] of overlap allowed by 2 features; by default O=0.1
-mismatch M mismatch penalty in exons when finding best mapping; by default M=2
-gap_open GO gap open penalty in exons when finding best mapping; by default GO=2
-gap_extend GE gap extend penalty in exons when finding best mapping; by default GE=1
-polish
-cds annotate status of each CDS (partial, missing start, missing stop, inframe stop codon)
-ad SOURCE, --annotation-database SOURCE
The source of the reference annotation (RefSeq / GENCODE / others).
Alignments:
-mm2_options =STR space delimited minimap2 parameters. By default ="-a --end-bonus 5 --eqx -N 50 -p 0.5"
-a A designate a feature mapped only if it aligns with coverage ≥A; by default A=0.5
-s S designate a feature mapped only if its child features (usually exons/CDS) align with sequence identity ≥S; by default S=0.5
-min_miniprot MIN_MINIPROT
The minimum length ratio of a protein-coding transcript to the longest protein-coding transcript within a gene locus, as identified
exclusively by miniprot in the target genome, is set by default to MIN_MINIPROT=0.9.
-max_miniprot MAX_MINIPROT
The maximum length ratio of a protein-coding transcript to the longest protein-coding transcript within a gene locus, as identified
exclusively by miniprot in the target genome, is set by default to MIN_MINIPROT=1.5.
-d D distance scaling factor; alignment nodes separated by more than a factor of D in the target genome will not be connected in the graph; by
default D=2.0
-flank F amount of flanking sequence to align as a fraction [0.0-1.0] of gene length. This can improve gene alignment where gene structure differs
between target and reference; by default F=0.0
