Main tool: Liftoff
Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.
liftoff GCA_000146045.2_R64_genomic.fna.gz GCA_000146045.2_R64_genomic.fna.gz -g GCA_000146045.2_R64_genomic.gff.gz
usage: liftoff [-h] (-g GFF | -db DB) [-o FILE] [-u FILE] [-exclude_partial] [-dir DIR] [-mm2_options =STR] [-a A] [-s S] [-d D] [-flank F] [-V] [-p P] [-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]
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 (annotation):
-g GFF annotation file to lift over in GFF or GTF format
-db DB name of feature database; if not specified, the -g argument must be provided and a database will be built automatically
Output:
-o FILE write output to FILE in same format as input; by default, output is written to terminal (stdout)
-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
-dir DIR name of directory to save intermediate fasta and SAM files; default is "intermediate_files"
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
-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
Miscellaneous settings:
-h, --help show this help message and exit
-V, --version show program version
-p P use p parallel processes to accelerate alignment; by default p=1
-m PATH Minimap2 path
-f 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)
Better documentation can be found at Liftoff