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author peterjc
date Mon, 30 Mar 2015 11:34:25 -0400
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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 contaimination present based on the species of the top BLAST hit 23 any major contamination present based on the species of the top BLAST hit
24 of 1000 representative sequences. 24 of 1000 representative sequences.
25 25
26 .. image:: https://raw.githubusercontent.com/peterjc/galaxy_blast/master/workflows/blast_top_hit_species/blast_top_hit_species.png 26 .. image:: https://raw.githubusercontent.com/peterjc/galaxy_blast/master/workflows/blast_top_hit_species/blast_top_hit_species.png
27 27
28 In words, the workflow proceeds as follows: 28 In words, the workflow proceeds as follows:
86 86
87 Disclaimer 87 Disclaimer
88 ========== 88 ==========
89 89
90 Species assignment by top BLAST hit is not suitable for any in depth 90 Species assignment by top BLAST hit is not suitable for any in depth
91 analysis. It is particularly prone to false positives where contaiminants 91 analysis. It is particularly prone to false positives where contaminants
92 in public datasets are mislabled. See for example Ed Yong (2015), 92 in public datasets are mislabelled. See for example Ed Yong (2015),
93 "There's No Plague on the NYC Subway. No Platypuses Either.": 93 "There's No Plague on the NYC Subway. No Platypuses Either.":
94 94
95 http://phenomena.nationalgeographic.com/2015/02/10/theres-no-plague-on-the-nyc-subway-no-platypuses-either/ 95 http://phenomena.nationalgeographic.com/2015/02/10/theres-no-plague-on-the-nyc-subway-no-platypuses-either/
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97 97