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annotate wtdbg2.xml @ 1:fe60b4299555 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
author mvdbeek
date Mon, 26 Nov 2018 09:10:05 -0500
parents 7bb3cf8b9a5d
children 79430547460a
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7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
mvdbeek
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1 <tool id="wtdbg2" name="wtdbg" version="2.2">
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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2 <description>De novo assembler for long noisy sequences</description>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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3 <requirements>
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4 <requirement type="package" version="2.2">wtdbg</requirement>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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5 <!-- Update this once 2.2 is released, need to create env manually for now
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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6 <requirement type="package" version="1.9">samtools</requirement>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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7 <requirement type="package" version="2.14">minimap2</requirement>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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8 -->
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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9 </requirements>
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10 <version_command>wtdbg2 -V</version_command>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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11 <command detect_errors="exit_code"><![CDATA[
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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12 wtdbg2 -t \${GALAXY_SLOTS:-1}
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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13 -i '$inputs'
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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14 -fo prefix
1
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15 #if $preset.select_preset != 'manual'
0
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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16 -x '$preset.select_preset'
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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17 #else
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18 -k $preset.kmer_length
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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19 -p $preset.hpc_kmer_length
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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20 -K $preset.high_freq_kmer
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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21 -E $preset.min_kmer_freq
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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22 -S $preset.sampling_rate
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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23 -l $preset.min_length_alignment
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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24 -m $preset.min_len_kmer_matching
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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25 -A $preset.keep_contained_reads_during_alignment
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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26 -s $preset.min_similarity
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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27 -L $preset.longest_subread
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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28 -e $preset.minimum_coverage_valid_edge
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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29 -g '$preset.approximate_genome_size'
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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30 -X $preset.best_layout_depth
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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31 #end if
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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32 && wtpoa-cns -t \${GALAXY_SLOTS:-1} -i prefix.ctg.lay -fo prefix.ctg.lay.fa &&
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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33 minimap2 -t \${GALAXY_SLOTS:-1} -x map-pb -a prefix.ctg.lay.fa '$inputs' | samtools view -Sb - >prefix.ctg.lay.map.bam &&
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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34 samtools sort prefix.ctg.lay.map.bam > prefix.ctg.lay.map.srt
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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35 #if $polish_consensus
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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36 && samtools view prefix.ctg.lay.map.srt.bam | wtpoa-cns -t \${GALAXY_SLOTS:-1} -d prefix.ctg.lay.fa -i - -fo prefix.ctg.lay.2nd.fa
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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37 #end if
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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38 ]]></command>
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39 <inputs>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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40 <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz" help="Select input reads"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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41 <conditional name="preset">
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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42 <param name="select_preset" type="select">
1
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43 <option value="rsII">PacBio RSII (-p 21 -S 4 -s 0.05 -L 5000)</option>
fe60b4299555 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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44 <option value="sequel">Pacbio Sequel (-p 0 -k 15 -AS 2 -s 0.05 -L 5000)</option>
fe60b4299555 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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45 <option value="nanopore">Nanopore (-p 19 -AS 2 -s 0.05 -L 5000)</option>
fe60b4299555 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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46 <option value="corrected">Corrected Reads (-p 0 -k 19 -AS 4 -s 0.5 -L 5000)</option>
0
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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47 <option value="manual">Specify Options</option>
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48 </param>
1
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49 <when value="rsII">
0
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50 </when>
1
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51 <when value="sequel">
0
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52 </when>
1
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53 <when value="nanopore">
0
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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54 </when>
1
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55 <when value="corrected">
0
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56 </when>
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57 <when value="manual">
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58 <param name="kmer_length" argument="-k" type="integer" value="0" min="0" max="25" label="kmer fsize"/>
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59 <param name="hpc_kmer_length" argument="-p" type="integer" value="0" min="0" max="25" label="kmer psize"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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60 <param name="high_freq_kmer" argument="-K" type="float" value="1000.05" label="Filter high frequency kmers, maybe repetitive" help=">= 1000 and indexing >= (1 - 0.05) * total_kmers_count"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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61 <param name="min_kmer_freq" argument="-E" type="integer" value="2" label="Min kmer frequency"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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62 <param name="sampling_rate" argument="-S" type="float" value="4.0" label="Subsampling kmers, 1/(S) kmers are indexed" help="-S is very useful in saving memeory and speeding up. Please note that subsampling kmers will have less matched length"/>
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63 <param name="min_length_alignment" argument="-l" type="integer" value="2048" label="Min length of alignment"/>
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64 <param name="min_length_kmer_matching" argument="-m" type="integer" value="200" label="Min matched length by kmer matching"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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65 <param name="keep_contained_reads_during_alignment" argument="-A" type="boolean" truevalue="-A" falsevalue="" label="Keep contained reads during alignment?"/>
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66 <param name="min_similarity" argument="-s" type="float" label="Min similarity, calculated by kmer matched length" value="0.05" min="0" max="1"/>
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67 <param name="longest_subread" argument="-L" type="integer" value="0" label="Choose the longest subread and drop reads shorter than this value"/>
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68 <param name="minimum_coverage_valid_edge" argument="-e" type="integer" value="3" label="Min read depth of a valid edge"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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69 <param name="approximate_genome_size" argument="-g" type="integer" value="0" label="Approximate genome size in Megabases"/>
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70 <param name="best_layout_depth" argument="-X" type="integer" value="50" min="1" label="Select best reads for this amount of coverage"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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71 </when>
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72 </conditional>
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73 <param name="polish_consensus" type="boolean" label="Polish consensus" help="Select No if you plan to use a different tool for polishing the contig consensus sequences"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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74 </inputs>
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75 <outputs>
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76 <data name="contigs" format="txt" from_work_dir="prefix.ctg.lay"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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77 <data name="consensus" format="fasta" from_work_dir="prefix.ctg.lay.fa"/>
7bb3cf8b9a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
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78 <data name="polished_consensus" format="fasta" from_work_dir="prefix.ctg.lay.2nd.fa"/>
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="inputs" value="ecoli-reads.fasta" ftype="fasta"/>
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83 <param name="preset|select_preset" value="rsII"/>
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84 <output name="contigs" value="contigs.txt"/>
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85 <output name="consensus" value="consensus.fa"/>
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86 <output name="polished_consensus" value="polished_consensus.fa"/>
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87 </test>
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88 </tests>
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89 <help><![CDATA[
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90 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.
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91
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92 During assembly, wtdbg2 chops reads into 1024bp segments, merges similar segments into a vertex and connects vertices based on the segment adjacency on reads. The resulting graph is called fuzzy Bruijn graph (FBG). It is akin to De Bruijn graph but permits mismatches/gaps and keeps read paths when collapsing k-mers. The use of FBG distinguishes wtdbg2 from the majority of long-read assemblers.
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93
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94 Wtdbg2 combines normal k-mers and homopolymer-compressed (HPC) k-mers to find read overlaps. Option -k specifies the length of normal k-mers, while -p specifies the length of HPC k-mers. By default, wtdbg2 samples a fourth of all k-mers by their hashcodes. For data of relatively low coverage, you may increase this sampling rate by reducing -S. This will greatly increase the peak memory as a cost, though. Option -e, which defaults to 3, specifies the minimum read coverage of an edge in the assembly graph. You may adjust this option according to the overall sequencing depth, too. Option -A also helps relatively low coverage data at the cost of performance. For PacBio data, -L5000 often leads to better assemblies emperically, so is recommended.
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95 ]]></help>
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96 <citations>
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97 </citations>
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98 </tool>