OPTIONS.md

Minimal options are:

lorean.py -pr <protein.fasta> -sp <species> <genome.fasta>

The specie name used in LoReAn needs to be in the AUGUSTUS database.

However, if RNA-seq is supplied, the tool will calculate the best AUGUSTUS sets using BRAKER1 software

Other options are:

-h, --help

 show help message and exit

-pr [PROTEINS], --proteins [PROTEINS]

Path to protein sequences FASTA file []

-sp [SPECIES], --species [SPECIES]

Species name for AUGUSTUS training. No re-training if species already present in AUGUSTUS config folder

-d, --stranded

Run LoReAn on stranded mode [FALSE]

-f, --fungus

Use this option for fungal species (used in Gene Mark-ES) [FALSE]

-k, --keep_tmp

Keep temporary files [FALSE]

-sr [FASTQ_file], --short_reads [FASTQ_file]

Path to short reads FASTQ. If paired end, comma- separated (1-1.fq,1-2.fq). BAM sorted files are allowed; the extension of the file should be filename.sorted.bam []

-lr [FASTQ_file], --long_reads [FASTQ_file]

Path to long reads FASTQ []

-a [FASTA_file], --adapter [FASTA_file]

FASTA file containing the adapter sequences. Adapter sequences in forward and reverse strain of the same
adapter need to be used in the file []

-rp [GFF_file], --repeat_masked [GFF_file]

GFF or GFF3 or GTF or BED file containing repeats
coordinates []

-u [GFF_file], --update [GFF_file]

GFF or GFF3 or GTF or BED file containing repeats
coordinates []

-m [MAX_LONG_READ], --max_long_read [MAX_LONG_READ]

Filter out long reads longer than this value (longer reads may affect mapping and assembling) [20000]

-pasa [PASA_DB], --pasa_db [PASA_DB]

PASA database name [pipeline_run]

-n [PREFIX_GENE], --prefix_gene [PREFIX_GENE]

Prefix to add to the final Gff3 gene name [specie]

-w [WORKING_DIR], --working_dir [WORKING_DIR]

Working directory (will create if not present) [./]

-t, --threads

Number of threads [3]

-cw N, --augustus_weigth N

Weight assigned to AUGUSTUS evidence for EVM [1]

-uw N, --update_weigth N

Weight assigned to GFF3 file to update for EVM [1]

-gw, --genemark_weigth

Weight assigned to GENEMARK evidence for EVM [1]

-tw, --trinity_weigth

Weight assigned to Trinity mapped with GMAP evidence for EVM [1]

-pw, --pasa_weigth

Weight assigned to PASA evidence for EVM [5]

-aw, --AAT_weigth

Weight assigned to AAT protein evidence for EVM [1]

-c, --segmentSize

Segment size for EVM partitions [100000]

-e, --overlapSize

Overlap size for EVM partitions [10000]

-g, --min_intron_length

Minimal intron length for GMAP [9]

-q, --max_intron_length

Maximal intron length for GMAP, STAR and TRINITY [1000]

-ee, --end_exon

Minimal length for end exon with GMAP [20]

-cme, --cluster_min_evidence

Minimal evidence needed to form a cluster [5]

-cMe, --cluster_max_evidence

Maximal evidence to form a cluster.Prevents the clustering or rRNA genes i.e. [5000]

-aol, --assembly_overlapLength

Minimal length (in nt) of overlap for ASSEMBLY [200]

-api, --assembly_percentIdentity

Minimal identity for the ASSEMBLY (95-100) [97]

-art, --assembly_readThreshold

Fraction of reads supporting an assembled UNITIG to keep on the ASSEMBLY (0.1-1) [0.3]

-v, --verbose

Prints out the commands used in LoReAn[FALSE]