USDA ARS VCRU Data Server
This web site, http://www.vcru.wisc.edu/sdata, contains data from the laboratory of Philipp W. Simon, USDA-ARS Vegetable Crops Research Unit [Click here for our web page]
 

Software from our lab

ExportText Excel macro

Roche 454 Utilities

bb.454contignet

bb.454contiginfo

Sequence Analysis Utilities

bb.motif

bb.orffinder

bb.fastareorder

MITOFY

Programs in the bb project are now stored on GitHub at https://github.com/dsenalik/bb

Roche 454 Utilities

bb.454contignet

Reference. If you use this software, you may cite using this reference:
Massimo Iorizzo, Douglas Senalik, Marek Szklarczyk, Dariusz Grzebelus, David Spooner and Philipp Simon
De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome
BMC Plant Biology 2012, 12:61

Download. Download bb.454contignet here - current version 1.0.7, May 4, 2012

Overview. This is a Perl program that will take an assembly of Roche 454 sequences generated by the Roche newbler/gsAssembler, and use the connection information to link generated contigs into a graphical map.

Description. A large amount of information about connections between various contigs in the gsAssembler assembly is contained in the 454ContigGraph.txt file generated by gsAssembler. I suggest looking at Lex Nederbragt's excellent description of the 454ContigGraph.txt file for more information about this file.

Thanks to Simon Gladman for adapting bb.454contignet to handle paired-end runs. Use the parameters --flowthrough, --flowbetween, --pairlinks, or --alllinks to visualize some or all of these additional types of connections

A prerequisite for this program is the availablility of the graphviz program neato, which is used to generate the actual image.
This is probably already installed on a standard Linux installation, but if not, the graphviz web size is http://www.graphviz.org/
On Fedora you would just type sudo yum install graphviz to install it,
or on Ubuntu sudo apt-get install graphviz

Important. An important point during the gsAssembler assembly is to save all contigs, no matter how small. Sometimes a very small, even as small as 1 b.p contig can be found connecting two larger contigs, so discarding small contigs could generate unnecessary gaps. Or, small indels between alleles could manifest themselves as very small contigs. So, when creating your assembly in gsAssembler, make sure to set the minimum contig size to 1 to avoid losing any useful data.

Example. Here is an example of a de novo chloroplast and mitochondrial genome assembly from a single region (half of a plate) of 454 whole-genome shotgun sequence:
This assembly and image were used, after some manual enhancements, in the publication cited above.

Example data files and commands:


Click on this image for a full-size version

Color names are listed at http://www.graphviz.org/doc/info/colors.html

Here is the full program syntax, which you can obtain by typing the name of the program with no parameters:

bb.454contignet  version 1.0.7
Required parameters:
  --indir=xxx       path to 454 assembly directory
  --outfile=xxx     output text file of results
  --contig=xxx[,xxx]...
                    one or more starting contig numbers,
                    separated by comma, or multiple --contig
                    parameters may be used. Use just the
                    numeric portion of the contig
Optional parameters:
  --type=xxx        output file format, default is "png"
                    ( anything besides "png" is experimental )
  --cmdfile=xxx     graphviz command file in .dot language will be created
                    using this name. If not specified, a temporary command
                    file will be created, and it will be deleted when done
  --imgfile=xxx     graph image file will be created with
                    this name. If not specified, will be
                    --outfile with .png extension added
  --fastaout=xxx    create a FASTA file of all contigs in
                    the output, save in this file
  --abyssexplorer=xxx  Generate a .dot file that can be used for
                    visualization with ABySS-Explorer 1.3.0,
                    http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer
  --flowthrough     include connection information derived from
                    reads that flow through more than two contigs
  --flowbetween[=x] include connection information derived from
                    reads that flow from one contig into another
                    by default, if the distance value is zero, it will not be
                    shown, the optional value for this parameter is a minimum
                    distance, defaulting to 1, set to --flowbetween=0 to show
                    these links also
  --pairlinks       include connection information derived
                    from paired end reads, only applicable for assemblies
                    containing paired end reads
  --alllinks        sets --flowthrough, --flowbetween, and --pairlinks
  --tag=tagname,contig[,contig]...  
                    list of 1 or more contigs will be given
                    this tag. Multiple --tag allowed.
                    tagname is a text label that will be shown
                    in the final image, e.g. --tag="ATP1,14,34"
  --label           a synonym for --tag
  --showbp          show length in b.p. in graph
  --shownt          a synonym for --showbp
  --showcoverage    show average contig read coverage in graph
  --color=colorname,contig[,contig]...  
                    like --tag, but color the contig.
                    for list of valid color names see
                    http://www.graphviz.org/doc/info/colors.html
  --forcelink=xxx-5:yyy-3   force a link where none exists
                    between specified ends, xxx and yyy are
                    contig numbers
  --level=xxx       maximum recursion level, default=2
  --boldabove=xxx   lines with read coverage >= this value
                    will be drawn in bold. no default value
  --exclude=xxx[,xxx]...
                    one or contigs to never traverse past,
                    for example a repeated region contig
  --listexcluded    print out a list of which excluded contigs
                    are being ignored
  --invert=xxx[,xxx]...
                    one or more contigs to plot backwards on
                    the graph, i.e. 3' to 5' direction
  --extend=xxx      auto extension for the single best
                    path, value is maximum steps, default=0
  --lowlimit=xxx    ignore connections < this number of reads
  --highlimit=xxx   ignore connections > this number of reads
  --len=xxx         len parameter to neato, default=1
  --nolabel         disable highlighting of dead ends, and limit
                    of recursion contigs
  --overlapmode     neato paramter, default is false, one of
                    none, true, scale
  --nospline        disable spline when edges would overlap
  --help            print this screen
  --quiet           only print error messages
  --debug           print extra debugging information

In place of lists of contigs, you can use @filename to read in
values for that parameter from a file, e.g. --exclude=@excl.txt

This program requires that the graphviz program "neato" be
available in the default PATH. The graphviz web site is
http://www.graphviz.org/

Version 1.0.7 adds experimental support for generation of a .dot file which can be used to visualize connections with ABySS-Explorer http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer

Some other keywords for search engines: Roche 454 graph image, graph structure, edges, contig linkages, contig links, contig network, linked contigs, fork

bb.454contiginfo

Download bb.454contiginfo here - current version 1.0, March 21, 2012

This is a Perl program that will take an assembly of Roche 454 sequences generated by the Roche newbler/gsAssembler, and displays all information for one or more specified contigs, in particular, the connection and read flowthrough information.

Here is the full program syntax, which you can obtain by typing the name of the program with no parameters:

bb.454contiginfo  version 1.0
This program analyzes some of the output files from a 454
assembly to find out everything available for a particular
contig. This information is all contained in the
454ContigGraph.txt file in the assembly directory.

Required parameters:
  --infile=xxx      input 454 assembly directory, or path
                    to 454ContigGraph.txt file
  --contig=xxx      contig to analyze ( multiple allowed )
                    use just the number e.g. --contig=123
                    or multiple numbers with , or ; as
                    separator, e.g. --contig=123,16389;599
  --outfile=xxx     output file name, use "-" for stdout
Optional parameters:
  --showscaffold    if contig is part of a scaffold, list
                    all contigs and gaps in that scaffold
  --help            print this screen
  --quiet           only print error messages
  --debug           print extra debugging information

Sequence Analysis Utilities

bb.motif

Download bb.motif here - current version 1.0, June 14, 2010

This program was used to generate a supplemental file for the publication:
Marina Iovene, Pablo F. Cavagnaro, Douglas Senalik, C. Robin Buell, Jiming Jiang and Philipp W. Simon
Comparative FISH mapping of Daucus species (Apiaceae family)
Chromosome Research Volume 19, Number 4, 493-506, DOI: 10.1007/s10577-011-9202-y

A copy of the output file from the above publication: 10577_2011_9202_MOESM2_ESM.txt

This program will take one or more sequences in a FASTA
file, and look for your specified motif sequence in them.

Required parameters:
  --motif=xxx        nucleotide sequence of the motif to find
  --infile=xxx       name of input FASTA file, multiple allowed
  --outfile=xxx      name of summary file to create
Optional parameters:
  --tbl2asnfile=xxx  create a feature table for tbl2asn import
  --tempdir=xxx      save intermediate files in this directory.
                     If not specified, temporary files are not kept
  --expect=xxx       expect value for blast, default = 10.0
  --debug            debugging mode=extra info printed, keep temp files
  --help             print this screen

bb.orffinder

Download bb.orffinder here - current version 1.3.0 - Apr 1, 2013

This is a Perl program that will computationally detect open reading frames in DNA or RNA sequences in FASTA format.
This is computationally similar to the NCBI program at http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi, but allows command-line automation of the process, as well as a few additional features.

This program will detect open reading frames in FASTA
DNA or RNA sequences. This is similar to the NCBI program at 
http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi

Required parameters:
  --infile=xxx       input file name
  --outfile=xxx      output file name, use "-" for stdout
Optional parameters:
  --fullstart        use full set of start codons: ATG GTG CTG TTG
                     the default is to only use ATG
  --anystart         start of sequence is also a valid orf start
  --minlen=xxx       minimum orf length in b.p., default=100
  --guessorientation guess orientation based on strand with the
                     most total orfs, this data will be be saved
                     instead of the list of orfs
  --fasta            output file is in FASTA format, each orf is
                     a separate sequence, information is in header
  --nonorffasta      second FASTA file with all sequence not in
                     the first one. File name is --outfile name
                     with "nonorf" inserted
  --fastacollapse    combine overlapping sequence in the FASTA file
  --fastalargest     if two orfs overlap, keep only the larger one
  --trimheader       remove any text in the FASTA header after 
                     the first occurrence of white space
  --origorder        return list in sequence order instead of
                     the default which is sorted by size
  --origorder=s      same, but do + and - strands separately
  --nsequence        include a column with nucleotide sequence
  --psequence        include a column with protein sequence
  --gffformat        generate output in gff3 format. This also
                     enables --trimheader
  --featureid=xxx    column 3 of gff file, default is "CDS"
  --non              do not allow any "N"s in an orf
  --help             print this screen
  --quiet            only print error messages
  --debug            print extra debugging information

bb.fastareorder

Download bb.fastareorder here - current version 1.0, September 3, 2011

This program will allow changing the order or orientation of multiple sequences in FASTA format, or extraction of a subset of sequences. The resulting sequences can optionally be concatenated into a single sequence.

bb.fastareorder  Version 1.0

Rearrange the order of sequences in a FASTA file based on
your specified contigs and orientations

Required parameters:
  --infile=xxx      input FASTA file name with multiple sequences
  --outfile=xxx     output file name, or "-" for stdout
  --seq=xxx         sequences to keep, multiple allowed, a plus
                    "+" for forward orientation is optional,
                    or use "-" anywhere to indicate reverse
                    complement. Use ".." to indicate a range.
                    Use "," to separate entries. Examples:
                    --seq=contig45 --seq=46,49,-21..23
                    --seq=+32 --seq=-65 --seq=76-
                    --seq=00021..45- -seq=45+..47
                    or use "s" for a spacer of 20 Ns
                    e.g. --seq=00021+,S,45-
                    The --seq parameter may be omitted if --exclude
                    or --random is used instead
Optional parameters:
  --exclude=xxx     use this in place of the --seq parameter to
                    output all contigs except these. Order will be
                    unchanged from the original file in this case.
  --random=xxx      return this many sequences selected at random
                    and placed in random order
  --coordinates     create this output file, which will store
                    the starting and ending position of each contig
  --onesequence     concatenate all sequences into one
  --blankline       for --onesequence mode, put a blank line
                    between each sequence
  --prefix=xxx      if using --onesequence, use this prefix,
                    default = "concatenated"
  --append          append to existing --outfile
  --startstop       add starting and ending base position
                    to FASTA headers
  --noqual          if a .qual file is present, a corresponding
                    output .qual file is created. This flag
                    turns off this quality file processing
  --help            print this screen
  --quiet           only print error messages
  --debug           print extra debugging information

MITOFY - Plant Mitochondrial Genome Annotaton

MITOFY was not created by us, but we provide a public web server that can be used to run a MITOFY analysis.
This page can be accessed at VCRU MITOFY Public Web Server
A download link may be found on that page.
The MITOFY home page is http://dogma.ccbb.utexas.edu/mitofy/

This page last modified Monday, 11-Aug-2014 20:16:55 CDT