annotate velvet_optimiser.xml @ 0:50ae1360fbbe default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

<tool id="velvetoptimiser" name="velvetoptimiser" version="1.0.0">
	<description>Auto optimise a genomic velvet assembly</description>
	<command interpreter="python">
	velvet_optimiser.py  '$start_hash_length' '$end_hash_length' 
	'#for $i in $inputs
		${i.file_format}
		${i.read_type}
		${i.input}
           #end for
	'
	'$threads'
	'1'
	'$kmeropt'
	'$covopt'
	'$contigs'
	'$LastGraph'
	'$velvet_asm'
	'$unused_reads_fasta'
	'$stats'
	'$othervelvetgoptions'
	'$contigs.extra_files_path'
	</command>

        <inputs>
          <param label="Start Hash Length" name="start_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Shorter hash lengths (i.e. less than 31) may cause out-of-memory problems.">

                        <option value="23">23</option>
                        <option value="25">25</option>
                        <option value="27">27</option>
                        <option value="29">29</option>
			<option value="31" selected="yes">31</option>
                        <option value="33">33</option>
                        <option value="35">35</option>
                        <option value="37">37</option>
                        <option value="39">39</option>
                        <option value="41">41</option>

          </param>
	 <param label="End Hash Length" name="end_hash_length" type="select" help="k-mer length in base pairs of the words being hashed.">
                        <option value="43">43</option>
                        <option value="45">45</option>
                        <option value="47">47</option>
                        <option value="49">49</option>
                        <option value="51">51</option>
                        <option value="53">53</option>
                        <option value="55">55</option>
                           <option value="57">57</option>
                         <option value="59">59</option>
                        <option value="61">61</option>
                        <option value="63">63</option>
                        <option value="65">65</option>
                        <option value="67">67</option>
			 <option value="69" selected="yes">69</option>

	 </param>

	 <param label="Number of threads" name="threads" type="select" help="Number of velvetg threads to run. Higher values will result in shorter run times but may cause an out of memory error. Select a lower value if this happens.">
                        <option value="1" selected="yes">1</option>
                        <option value="2">2</option>
                        <option value="3">3</option>
                        <option value="4">4</option>

         </param>
  	<param label="Kmer optimisation metric" name="kmeropt" type="select" help="Metric used to identify the optimal kmer size.">
                        <option value="Lbp">Total number of bp in contigs >1kb</option>
                        <option value="Lcon">Number of contigs >1kb</option>
                        <option value="max">Length of single longest contig</option>
                        <option value="n50" selected="yes">N50 size</option>
			 <option value="ncon">Total number of contigs</option>
			 <option value="tbp">Total number of bp in contigs of any size</option>

         </param>

	 <param label="Coverage optimisation metric" name="covopt" type="select" help="Metric used to identify the optimal coverage cutoff in velvetg.">
                        <option value="Lbp" selected="yes">Total number of bp in contigs >1kb</option>
                        <option value="Lcon">Number of contigs >1kb</option>
                        <option value="max">Length of single longest contig</option>
                        <option value="n50">N50 size</option>
                         <option value="ncon">Total number of contigs</option>
                         <option value="tbp">Total number of bp in contigs of any size</option>

         </param>

	<param label="Advanced velvetg options" name="othervelvetgoptions" title="Advanced velvetg options" help="Other Velvetg options - see below for details" type="text" size="30">
		
	</param>
    <!--      <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/> -->
          <repeat name="inputs" title="Input Files">
                      <param label="file format" name="file_format" type="select">
                              <option value="-fasta" selected="yes">fasta</option>
                              <option value="-fastq">fastq</option>
                              <option value="-eland">eland</option>
                              <option value="-gerald">gerald</option>
                      </param>
                      <param label="read type" name="read_type" type="select">
                              <option value="-short" selected="yes">short reads</option>
                              <option value="-shortPaired">shortPaired reads</option>
                              <option value="-short2">short2 reads</option>
                              <option value="-shortPaired2">shortPaired2 reads</option>
                              <option value="-long">long reads (reads >200bp e.g. 454 reads)</option>
                              <option value="-longPaired">longPaired reads</option>
                      </param>


            <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/>
          </repeat>
        </inputs>
	
	<outputs>

	        <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs"/>
                       <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads">
                 <!--  <filter>unused_reads['generate_unused'] == "yes"</filter>-->
                </data>
               
                <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads">
                 <!--  <filter>unused_reads['generate_unused'] == "yes"</filter>-->
                </data>
                <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats"/>
   		  <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg">
                  <!-- <filter>generate_amos['afg'] == "yes"</filter> -->
                </data>

  		  <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph">
		    <!-- <filter>last_graph['generate_graph'] == "yes"</filter> -->
                </data>

            
	</outputs>
	<requirements>
		<requirement type="package">velvet</requirement>
	</requirements>
	
	<help>
**Velvet Optimiser Overview**

Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.

Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Read the Velvet `documentation`__ for details on using the Vevlet Assembler.

.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/

.. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf

------

**VelvetOptimiser**

VelvetOptimiser was originally written by Simon Gladman of CSIRO.

VelvetOptimiser performs a number of velveth and velvetg steps to try and optimise an assembly based on the metrics provided below. 

------

**Outputs**


**Contigs**

The *contigs.fa* file.
This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig lgth threshold, then the contigs shorter than that value are omitted.
Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively.
The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's.

**Stats**

The *stats.txt* file.
This file is a simple tabbed-delimited description of the nodes. The column names are pretty much self-explanatory. Note however that node lengths are given in k-mers. To obtain the length in nucleotides of each node you simply need to add k - 1, where k is the word-length used in velveth.
The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively.
The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1).
Also, the difference between # cov and # Ocov is the way these values are computed. In the first count, slightly divergent sequences are added to the coverage tally. However, in the second, stricter count, only the sequences which map perfectly onto the consensus sequence are taken into account.

**LastGraph**

The *LastGraph* file.
This file describes in its entirety the graph produced by Velvet.

**AMOS.afg**
The *velvet_asm.afg* file.
This file is mainly designed to be read by the open-source AMOS genome assembly package. Nonetheless, a number of programs are available to transform this kind of file into other assembly file formats (namely ACE, TIGR, Arachne and Celera). See http://amos.sourceforge.net/ for more information.
The file describes all the contigs contained in the contigs.fa file (cf 4.2.1).

**Advanced options**
        -scaffolding  yes|no             : scaffolding of contigs used paired end information (default: on)
        -max_branch_length  integer      : maximum length in base pair of bubble (default: 100)
        -max_divergence  floating-point  : maximum divergence rate between two branches in a bubble (default: 0.2)
        -max_gap_count  integer          : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
        -min_pair_count  integer         : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)
        -max_coverage  floating point    : removal of high coverage nodes AFTER tour bus (default: no removal)
        -long_mult_cutoff  int           : minimum number of long reads required to merge contigs (default: 2)



**Hash Length**

The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed. 

The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::

# it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
# it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
# it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.

Now you still have quite a lot of possibilities. As is often the case, it's a trade- off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below). . . so there's a sweet spot to be found with time and experience.
We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C # (L - k + 1)/L where k is your hash length, and L you read length.
Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run! VelvetOptimiser automates these tests for you.


**Velvetg options**



**Input Files**

Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.

Supported file formats are::

  fasta
  fastq 
  eland
  gerald

Read categories are::

  short (default)
  shortPaired
  short2 (same as short, but for a separate insert-size library - i.e. if you have two libraries of different lengths)
  shortPaired2 (see above)
  long (for Sanger, 454 or even reference sequences)
  longPaired

	</help>
</tool>