Mercurial > repos > iuc > megahit_contig2fastg
annotate megahit_contig2fastg.xml @ 1:b910d0cbc00b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit b1f8042755de7bba00870a39e4352b07d5fd0422
author | iuc |
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date | Sun, 24 Mar 2019 11:25:07 -0400 |
parents | ed22349139ee |
children | 4ec5b3777508 |
rev | line source |
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ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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1 <tool id="megahit_contig2fastg" name="megahit contig2fastg" version="@VERSION@+@GALAXY_VERSION@"> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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2 <description>for converting MEGAHIT's contigs (.fa) to assembly graphs (.fastg)</description> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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3 <macros> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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4 <token name="@GALAXY_VERSION@">galaxy1</token> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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5 <token name="@VERSION@">1.1.3</token> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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6 </macros> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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7 <requirements> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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8 <requirement type="package" version="@VERSION@">megahit</requirement> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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9 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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10 <version_command>megahit --version</version_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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11 <command detect_errors="exit_code"><![CDATA[ |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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12 megahit_toolkit contig2fastg |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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13 '${kmer}' |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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14 '${contigs}' > '${fastg}' |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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15 ]]></command> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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16 <inputs> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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17 <param name="contigs" type="data" format="fasta" label="Contig file" help="Ex: k99.contigs.fa" /> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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18 <param name="kmer" type="integer" value="99" label="K-mer length" help="Usually indicated within the filename (when derived from MEGAHIT)"/> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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19 </inputs> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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20 <outputs> |
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b910d0cbc00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit b1f8042755de7bba00870a39e4352b07d5fd0422
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21 <data format="fastg" name="fastg" label="Assembly graph via ${tool.name} on ${on_string}" /> |
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ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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22 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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23 <tests> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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24 <test> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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25 <param name="contigs" value="k21.contigs.fa" ftype="fasta" /> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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26 <param name="kmer" value="21"/> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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27 <output name="fastg"> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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28 <assert_contents> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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29 <has_text text=">NODE_1_length_576" /> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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30 </assert_contents> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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31 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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32 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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33 </tests> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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34 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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35 |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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36 **MEGAHIT toolkit's contig2fastg** |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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37 |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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38 Contig2fastg is a subprogram within the MEGAHIT toolkit. It converts MEGAHIT's contigs (.fa) to assembly graphs (.fastg) that can be utilized for protein/peptide identification via graph2pro and can also be visualized via Bandage. |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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39 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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40 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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41 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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42 **EXAMPLE** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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43 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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44 *Command:* |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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45 |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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46 megahit_toolkit contig2fastg 99 intermediate_contigs/k99.contigs.fa > k99.contigs.fastg |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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47 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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48 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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49 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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50 *k99.contigs.fa* |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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51 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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52 >k21_1 flag=3 multi=1.0486 len=576 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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53 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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54 CGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTC... |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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55 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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56 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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57 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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58 *k99.contigs.fastg* |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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59 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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60 >NODE_1_length_576_cov_1.0486_ID_1:NODE_1_length_576_cov_1.0486_ID_1; |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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61 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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62 CGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTC... |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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63 |
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64 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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65 |
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66 **MEGAHIT** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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67 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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68 MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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69 |
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70 -------- |
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71 |
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72 **Project links:** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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73 |
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74 MEGAHIT: https://github.com/voutcn/megahit |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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75 |
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76 MEGAHIT Toolkit: https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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77 |
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78 Graph2Pro-Var: https://github.com/COL-IU/graph2pro-var |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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79 |
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80 Bandage: http://rrwick.github.io/Bandage/ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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81 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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82 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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83 ]]></help> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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84 <citations> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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85 <citation type="doi">10.1093/bioinformatics/btv033</citation> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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86 </citations> |
ed22349139ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg commit 9953444ccbe61c186bdfcb341dc000d2545e73f1
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87 </tool> |