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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
author peterjc
date Wed, 09 Sep 2020 15:13:58 +0000
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13 13
14 This is an example workflow using the Galaxy wrappers for NCBI BLAST+, 14 This is an example workflow using the Galaxy wrappers for NCBI BLAST+,
15 see https://github.com/peterjc/galaxy_blast 15 see https://github.com/peterjc/galaxy_blast
16 16
17 17
18 Galaxy workflow for counting species of top BLAST hits 18 Galaxy workflow for counting species of top BLAST hits
19 ====================================================== 19 ======================================================
20 20
21 This Galaxy workflow (file ``blast_top_hit_species.ga``) is intended for an 21 This Galaxy workflow (file ``blast_top_hit_species.ga``) is intended for an
22 initial assessment of a transcriptome assembly to give a crude indication of 22 initial assessment of a transcriptome assembly to give a crude indication of
23 any major contamination present based on the species of the top BLAST hit 23 any major contamination present based on the species of the top BLAST hit
40 sequences to give a new tabular file with exactly 1000 lines, adding 40 sequences to give a new tabular file with exactly 1000 lines, adding
41 ``None`` for sequences missing a BLAST hit. 41 ``None`` for sequences missing a BLAST hit.
42 7. Count the BLAST species names in this file. 42 7. Count the BLAST species names in this file.
43 8. Sort the counts. 43 8. Sort the counts.
44 44
45 Finally we would suggest visualising the sorted tally table as a Pie Chart. 45 Finally we would suggest visualising the sorted tally table as a Pie Chart,
46 as in the example below.
46 47
47 48
48 Sample Data 49 Sample Data
49 =========== 50 ===========
50 51
51 As an example, you can upload the transcriptome assembly of the nematode 52 As an example, you can upload the transcriptome assembly of the nematode
52 *Nacobbus abberans* from Eves van den Akker *et al.* (2015), 53 *Nacobbus abberans* from Eves van den Akker *et al.* (2015),
53 http://dx.doi.org/10.1093/gbe/evu171 using this URL: 54 https://doi.org/10.1093/gbe/evu171 using this URL:
54 55
55 http://nematode.net/Data/nacobbus_aberrans_transcript_assembly/N.abberans_reference_no_contam.zip 56 http://nematode.net/Data/nacobbus_aberrans_transcript_assembly/N.abberans_reference_no_contam.zip
56 57
57 Running this workflow with a copy of the NCBI non-redundant ``nr`` database 58 Running this workflow with a copy of the NCBI non-redundant ``nr`` database
58 from 16 Oct 2014 (which did **not** contain this *N. abberans* dataset) gave 59 from 16 Oct 2014 (which did **not** contain this *N. abberans* dataset) gave
70 5 eudicots 71 5 eudicots
71 5 flies 72 5 flies
72 ... ... 73 ... ...
73 ===== ================== 74 ===== ==================
74 75
75 As you might guess from the filename ``N.abberans_reference_no_contam.fasta``, 76 As you might guess from the filename ``N.abberans_reference_no_contam.fasta``,
76 this transcriptome assembly has already had obvious contamination removed. 77 this transcriptome assembly has already had obvious contamination removed.
77 78
78 At the time of writing, Galaxy's visualizations could not be included in 79 At the time of writing, Galaxy's visualizations could not be included in
79 a workflow. You can generate a pie chart from the final count file using 80 a workflow. You can generate a pie chart from the final count file using
80 the counts (c1) and labels (c2), like this: 81 the counts (c1) and labels (c2), like this:
140 141
141 142
142 Availability 143 Availability
143 ============ 144 ============
144 145
145 This workflow is available to download and/or install from the main Galaxy Tool Shed: 146 This workflow is available from myExperiment:
147
148 http://www.myexperiment.org/workflows/4637
149
150 You can also download and/or install it from the main Galaxy Tool Shed:
146 151
147 http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species 152 http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species
148 153
149 Test releases (which should not normally be used) are on the Test Tool Shed: 154 Test releases (which should not normally be used) are on the Test Tool Shed:
150 155
156 161
157 162
158 Citation 163 Citation
159 ======== 164 ========
160 165
161 Please cite the following paper (currently available as a preprint): 166 Please cite the following paper:
162 167
163 NCBI BLAST+ integrated into Galaxy. 168 NCBI BLAST+ integrated into Galaxy.
164 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo 169 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo.
165 bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint) 170 GigaScience 2015, 4:1.
171 https://doi.org/10.1186/s13742-015-0080-7
166 172
167 You should also cite Galaxy, and the NCBI BLAST+ tools: 173 You should also cite Galaxy, and the NCBI BLAST+ tools:
168 174
169 BLAST+: architecture and applications. 175 BLAST+: architecture and applications.
170 C. Camacho et al. BMC Bioinformatics 2009, 10:421. 176 C. Camacho et al. BMC Bioinformatics 2009, 10:421.
171 DOI: http://dx.doi.org/10.1186/1471-2105-10-421 177 https://doi.org/10.1186/1471-2105-10-421
172 178
173 179
174 Automated Installation 180 Automated Installation
175 ====================== 181 ======================
176 182
186 ======= 192 =======
187 193
188 ======= ====================================================================== 194 ======= ======================================================================
189 Version Changes 195 Version Changes
190 ------- ---------------------------------------------------------------------- 196 ------- ----------------------------------------------------------------------
191 v0.1.0 - Initial Tool Shed release, targetting NCBI BLAST+ 2.2.29 197 v0.1.0 - Initial MyExperiment and Tool Shed release.
198 - Targetting NCBI BLAST+ 2.2.29
192 ======= ====================================================================== 199 ======= ======================================================================
193 200
194 201
195 Developers 202 Developers
196 ========== 203 ==========