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]