art - Online in the Cloud

PROGRAM:

NAME

art - Artemis genome browser and annotation tool

SYNOPSIS

art [options] SEQUENCE_FILE [+FEATURE_FILE...]

OPTIONS

SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file
FEATURE_FILE An Artemis TAB file, or GFF file

-options FILE Read a text file of options from FILE
-debug Run using the debugging JVM instead
-fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit
pointers

-Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
-Doffset=XXX Open viewer at base position XXX [integer >= 1]
-Duserplot=FILE[,FILE2] Open one or more userplots
-Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data)
-Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files
-DbamClone=n Open all BAMs in multiple (n > 1) panels
-Dbam[1,2,..]=FILE[,FILE2,..] Open BAMs in separate panels
-Dshow_snps Show SNP marks in BamView
-Dshow_snp_plot Open SNP plot in BamView
-Dshow_cov_plot Open coverage plot in BamView
-Dshow_forward_lines=? Hide/show forward frame lines [true,false]
-Dshow_reverse_lines=? Hide/show reverse frame lines [true,false]
-Dchado="h:p/d?u" Get Artemis to open this CHADO database
-Dread_only Open CHADO database read-only

EXAMPLES

% art AJ006275.embl
% art contigs.fa +annotation.gff +islands.tab
% art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk
% art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3

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