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Jon PalmerJon Palmer
Jon Palmer
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update commands docs
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‎docs/commands.rst

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@@ -13,7 +13,7 @@ Funannotate is a series of Python scripts that are launched from a Python wrappe
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$ funannotate
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Usage: funannotate <command> <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Funannotate is a genome prediction, annotation, and comparison pipeline.
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Usage: funannotate clean <arguments>
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version: 0.8.0
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version: 1.0.1
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Description: The script sorts contigs by size, starting with shortest contigs it uses Mummer
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to find contigs duplicated elsewhere, and then removes duplicated contigs.
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Usage: funannotate clean <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: The script sorts contigs by size, starting with shortest contigs it uses Mummer
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to find contigs duplicated elsewhere, and then removes duplicated contigs.
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Description: This script sorts the input contigs by size (longest->shortest) and then relabels
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the contigs with a simple name (e.g. scaffold_1). Augustus can have problems with
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some complicated contig names.
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Arguments: -i, --input Multi-fasta genome file (Required)
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-o, --out Cleaned multi-fasta output file (Required)
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-p, --pident Percent identity of overlap. Default = 95
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-c, --cov Percent coverage of overlap. Default = 95
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-m, --minlen Minimum length of contig to keep. Default = 500
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--exhaustive Test every contig. Default is to stop at N50 value.
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Arguments: -i, --input Multi-fasta genome file. (Required)
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-o, --output Sorted by size and relabeled output file. (Required)
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-b, --base Base name to relabel contigs. Default: scaffold
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--minlen Shorter contigs are discarded. Default: 0
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funannotate species
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Usage: funannotate train <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script is a wrapper for genome-guided Trinity followed by PASA. Dependencies are
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Hisat2, Trinity, Samtools, Fasta, GMAP, Blat, MySQL, PASA. RapMap is optional but will
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Usage: funannotate predict <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script takes genome multi-fasta file and a variety of inputs to do a comprehensive whole
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genome gene model prediction. Uses AUGUSTUS, GeneMark, BUSCO, BRAKER1, EVidence Modeler,
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-s, --species Species name, use quotes for binomial, e.g. "Aspergillus fumigatus"
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Optional: --isolate Isolate name, e.g. Af293
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--strain Strain name.
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--strain Strain name, e.g. FGSCA4
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--name Locus tag name (assigned by NCBI?). Default: FUN_
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--numbering Specify where gene numbering starts. Default: 1
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--maker_gff MAKER2 GFF file. Parse results directly to EVM.
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--pasa_gff PASA generated gene models. filename:weight
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--other_gff Annotation pass-through to EVM. filename:weight
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Usage: funannotate fix <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script takes a GenBank genome annotation file and an NCBI tbl file to
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generate updated annotation. Script is used to fix problematic gene models
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Usage: funannotate update <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script will run PASA mediated update of gene models. It can directly update
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the annotation from an NCBI downloaded GenBank file using RNA-seq data or can be
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--single_norm Normalized single-ended FASTQ reads
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--trinity Pre-computed Trinity transcripts (FASTA)
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--jaccard_clip Turn on jaccard clip for dense genomes [Recommended for fungi]
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--pasa_gff PASA/Transdecoder GFF
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--pasa_config PASA assembly config file
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--kallisto Kallisto abundance tsv table
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--pasa_config PASA assembly config file, i.e. from previous PASA run.
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--no_antisense_filter Skip anti-sense filtering.
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--no_normalize_reads Skip read Normalization
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--no_trimmomatic Skip Quality Trimming of reads
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Usage: funannotate remote <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script runs remote server functional annotation for Phobius, InterProScan5, and
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antiSMASH (fungi). These searches are slow, if you can setup these services locally
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Usage: funannotate annotate <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script functionally annotates the results from funannotate predict. It pulls
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annotation from PFAM, InterPro, EggNog, UniProtKB, MEROPS, CAZyme, and GO ontology.
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or
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--gff Genome GFF3 annotation file
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--fasta Genome in multi-fasta format
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--proteins Genome proteins in multi-fasta format
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-s, --species Species name, use quotes for binomial, e.g. "Aspergillus fumigatus"
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-o, --out Output folder for results
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Optional: --sbt NCBI submission template file. (Recommended)
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-a, --annotations Custom annotations (3 column tsv file)
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--eggnog Eggnog-mapper annotations file.
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--antismash antiSMASH secondary metabolism results, GBK file.
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--iprscan InterProScan XML file
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--phobius Phobius pre-computed results (-short output)
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--eggnog Eggnog-mapper annotations file (if NOT installed)
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--antismash antiSMASH secondary metabolism results (GBK file from output)
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--iprscan InterProScan5 XML file
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--phobius Phobius pre-computed results (if phobius NOT installed)
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--isolate Isolate name
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--strain Strain name
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--busco_db BUSCO models. Default: dikarya
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Usage: funannotate compare <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script does light-weight comparative genomics between funannotated genomes. Output
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is graphs, phylogeny, CSV files, etc --> visualized in web-browser.
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Usage: funannotate setup <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Script will download/format necessary databases for funannotate.
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Usage: funannotate outgroups <arguments>
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version: 1.0.0
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version: 1.0.1
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Description: Managing the outgroups folder for funannotate compare
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