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/tools/sr_assembly/velveth.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="velveth" name="velveth" version="1.0.0">
  2  <description>Prepare a dataset for the Velvet velvetg Assembler</description>
  3  <version_command>velveth 2&gt;&amp;1 | grep "Version" | sed -e 's/Version //'</version_command>
  4  <command interpreter="python">
  5    velveth_wrapper.py 
  6           '$out_file1' '$out_file1.extra_files_path'
  7           $hash_length
  8           $strand_specific
  9           #for $i in $inputs
 10                ${i.file_format}
 11                ${i.read_type}
 12                ${i.input}
 13           #end for
 14  </command>
 15  <inputs>
 16    <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed.">
 17      <option value="11">11</option>
 18      <option value="13">13</option>
 19      <option value="15">15</option>
 20      <option value="17">17</option>
 21      <option value="19">19</option>
 22      <option value="21" selected="yes">21</option>
 23      <option value="23">23</option>
 24      <option value="25">25</option>
 25      <option value="27">27</option>
 26      <option value="29">29</option>
 27    </param>
 28    <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."/>
 29    <repeat name="inputs" title="Input Files">
 30      <param label="file format" name="file_format" type="select">
 31        <option value="-fasta" selected="yes">fasta</option>
 32        <option value="-fastq">fastq</option>
 33        <option value="-eland">eland</option>
 34        <option value="-gerald">gerald</option>
 35      </param>
 36      <param label="read type" name="read_type" type="select">
 37        <option value="-short" selected="yes">short reads</option>
 38        <option value="-shortPaired">shortPaired reads</option>
 39        <option value="-short2">short2 reads</option>
 40        <option value="-shortPaired2">shortPaired2 reads</option>
 41        <option value="-long">long reads</option>
 42        <option value="-longPaired">longPaired reads</option>
 43      </param>
 44
 45      <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/>
 46    </repeat>
 47  </inputs>
 48  <outputs>
 49    <data format="velvet" name="out_file1" />
 50  </outputs>
 51  <requirements>
 52    <requirement type="package">velvet</requirement>
 53  </requirements>
 54  <tests>
 55    <test>
 56      <param name="hash_length" value="21" />
 57      <param name="read_type" value="-shortPaired" />
 58      <!-- <repeat name="inputs"> -->
 59      <param name="file_format" value="fasta" />
 60      <param name="read_type" value="shortPaired reads" />
 61      <param name="input" value="velvet_test_reads.fa" ftype="fasta" />
 62      <!-- </repeat> -->
 63      <param name="strand_specific" value="" />
 64      <output name="out_file1" file="velveth_test1/output.html" lines_diff="4">
 65        <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" />
 66        <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" />
 67      </output>
 68    </test>
 69  </tests>
 70  <help>
 71**Velvet Overview**
 72
 73Velvet_ 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.
 74
 75Velvet 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.
 76
 77Read the Velvet `documentation`__ for details on using the Velvet Assembler.
 78
 79.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
 80
 81.. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
 82
 83------
 84
 85**Velveth**
 86
 87Velveth takes in a number of sequence files, produces a hashtable, then outputs two files in an output directory (creating it if necessary), Sequences and Roadmaps, which are necessary to velvetg.
 88
 89------
 90
 91**Hash Length**
 92
 93The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed. 
 94
 95The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::
 96
 97# it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
 98# it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
 99# it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
100
101Now 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.
102We 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.
103Experience 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!
104
105**Input Files**
106
107Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
108read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.
109
110Supported file formats are::
111
112  fasta
113  fastq 
114  fasta.gz 
115  fastq.gz 
116  eland
117  gerald
118
119Read categories are::
120
121  short (default)
122  shortPaired
123  short2 (same as short, but for a separate insert-size library)
124  shortPaired2 (see above)
125  long (for Sanger, 454 or even reference sequences)
126  longPaired
127
128  </help>
129</tool>