The MAKER control files explained

MAKER is given all of the information it needs to run through three control files, maker_opts.ctl, maker_bopts.ctl, and maker_exe.ctl. Each file contains many options, some are essential for MAKER to run and others are there to help MAKER run better on your species. Making informed thoughtful decisions when setting control file options will result in a more accurate annoatation for most species than simply accepting the defaults. Now lets go through the files.

maker_opts.ctl

The maker_opts.ctl file is the workhorse of the control files and where the vast majority of the parameters are set so here we go line by line.

#-----Genome (Required for De-Novo Annotation)

genome= #genome sequence (fasta format or fasta embeded in GFF3)

organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----Re-annotation Using MAKER Derived GFF3

maker_gff= #re-annotate genome based on this gff3 file

est_pass=0 #use ests in maker_gff: 1 = yes, 0 = no

altest_pass=0 #use alternate organism ests in maker_gff: 1 = yes, 0 = no

protein_pass=0 #use proteins in maker_gff: 1 = yes, 0 = no

rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no

model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no

pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no

other_pass=0 #passthrough everything else in maker_gff: 1 = yes, 0 = no

#-----EST Evidence (for best results provide a file for at least one)

est= #non-redundant set of assembled ESTs in fasta format (classic EST analysis)

altest= #EST/cDNA sequence file in fasta format from an alternate organism

est_gff= #EST evidence from an external gff3 file

altest_gff= #Alternate organism EST evidence from a separate gff3 file

#-----Protein Homology Evidence (for best results provide a file for at least one)

protein=  #protein sequence file in fasta format

protein_gff=  #protein homology evidence from an external gff3 file

#-----Repeat Masking (leave values blank to skip repeat masking)

model_org=all #select a model organism for RepBase masking in RepeatMasker

rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker

repeat_protein=/Users/mcampbell/maker/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner

rm_gff= #repeat elements from an external GFF3 file

prok_rm=0 #forces MAKER to run repeat masking on prokaryotes (don't change this), 1 = yes, 0 = no

softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

#-----Gene Prediction

snaphmm= #SNAP HMM file

gmhmm= #GeneMark HMM file

augustus_species= #Augustus gene prediction species model

fgenesh_par_file= #Fgenesh parameter file

pred_gff= #ab-initio predictions from an external GFF3 file

model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)

est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no

protein2genome=0 #gene prediction from protein homology, 1 = yes, 0 = no

unmask=0 #Also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no

#-----Other Annotation Feature Types (features MAKER doesn't recognize)

other_gff= #features to pass-through to final output from an extenal GFF3 file

#-----External Application Behavior Options

alt_peptide=C #amino acid used to replace non standard amino acids in BLAST databases

cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)

#-----MAKER Behavior Options

max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases  memory usage)

min_contig=1 #skip genome contigs below this length (under 10kb are often useless)

pred_flank=200 #flank for extending evidence clusters sent to gene predictors

pred_stats=0 #report AED and QI statistics for all predictions as well as models

AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)

min_protein=0 #require at least this many amino acids in predicted proteins

alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no

always_complete=0 #force start and stop codon into every gene, 1 = yes, 0 = no

map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no

keep_preds=0 #Add unsupported gene prediction to final annotation set, 1 = yes, 0 = no

split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)

single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no

single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'

correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes

tries=2 #number of times to try a contig if there is a failure for some reason

clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no

clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no

TMP= #specify a directory other than the system default temporary directory for temporary files

#-----EVALUATOR Control Options

evaluate=0 #run EVALUATOR on all annotations (very experimental), 1 = yes, 0 = no

side_thre=5

eva_window_size=70

eva_split_hit=1

eva_hspmax=100

eva_gspmax=100

enable_fathom=0