A rust library for preparing expanded transcriptome references for quantification with alevin-fry.
To use outside of simpleaf, follow the following help message:
build the (expanded) reference index
Usage: roers make-ref [OPTIONS] <GENOME> <GENES> <OUT_DIR>
Arguments:
<GENOME> The path to a genome fasta file
<GENES> The path to a gene annotation gtf/gff3 file
<OUT_DIR> The path to the output directory (will be created if it doesn't exist)
Options:
-a, --aug-type <AUG_TYPE>
Comma separated types of augmented sequences to include in the output FASTA file on
top of spliced transcripts. Available options are `intronic` (or `i` for short),
`gene-body` (or `g`), and `transcript-body` (or `t`)
--dedup
Indicates whether identical sequences will be deduplicated
-p, --filename-prefix <FILENAME_PREFIX>
The file name prefix of the generated output files [default: roers_ref]
--no-transcript
A flag of not including spliced transcripts in the output FASTA file. (usually there
should be a good reason to do so)
--gff3
Denotes that the input annotation is a GFF3 (instead of GTF) file
-h, --help
Print help
-V, --version
Print version
Intronic Sequence Options:
-r, --read-length <READ_LENGTH>
The read length of the single-cell experiment being processed (determines flank size)
[default: 91]
--flank-trim-length <FLANK_TRIM_LENGTH>
Determines the length of sequence subtracted from the read length to obtain the flank
length [default: 5]
--no-flanking-merge
Indicates whether flank lengths will be considered when merging introns
Extra Spliced Sequence File:
--extra-spliced <EXTRA_SPLICED> The path to an extra spliced sequence fasta file
Extra Unspliced Sequence File:
--extra-unspliced <EXTRA_UNSPLICED> The path to an extra unspliced sequence fasta file