Auden Cote-L'Heureux
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4e1ceae627
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Delete Utilities/for_trees/ColorByClade_v2.0.py
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2023-11-27 13:54:09 -05:00 |
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Auden Cote-L'Heureux
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3dd53c1eb9
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Fixing rooting & ladderizing & node labels
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2023-11-27 13:53:02 -05:00 |
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Auden Cote-L'Heureux
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8872d1724d
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Update preguidance.py
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2023-11-24 12:35:21 -05:00 |
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Auden Cote-L'Heureux
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8fa40adf9c
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Adding version of contamination loop before November mods
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2023-11-22 11:41:05 -05:00 |
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MCLeleu
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e082b6bf3a
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Rename rename_tip_labels .py to rename_tip_labels.py
Removed a space in the filename
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2023-11-15 16:41:31 +01:00 |
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Godwin Ani
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f292cf3cf9
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Add files via upload
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2023-11-13 16:25:52 -05:00 |
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Auden Cote-L'Heureux
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1b587bf266
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Version of scripts used to successfully run conserved OGs on 11/13/23
Recent updates:
Similarity filter adjusted to have on/off parameter
Blacklist implemented & tested
Output list of Guidance-removed sequences with seq scores
Temp/intermediate file naming issue fixed
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2023-11-13 12:09:57 -05:00 |
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Auden Cote-L'Heureux
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842b229833
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Rename 6_SummaryStats.py to 5b_SummaryStats.py
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2023-11-10 10:21:35 -05:00 |
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Auden Cote-L'Heureux
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06e13e7caa
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Rename 5_FinalizeName.py to 5a_FinalizeName.py
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2023-11-10 10:21:24 -05:00 |
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Godwin Ani
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c300980148
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f/paralogs assessment script
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2023-11-07 11:44:36 -05:00 |
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Godwin Ani
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b8436d03dd
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For adding metadata to tree tip labels
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2023-11-06 10:15:53 -05:00 |
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Auden Cote-L'Heureux
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43a7439a02
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Adjusting sim filter, adding score to guidance removed seqs output
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2023-11-03 11:05:46 -04:00 |
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Auden Cote-L'Heureux
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72660b742b
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Adding CheckSetup.py to the Genomes
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2023-10-30 17:18:56 -04:00 |
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Auden Cote-L'Heureux
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fbac4f6b09
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Add files via upload
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2023-10-30 16:40:40 -04:00 |
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Auden Cote-L'Heureux
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b8ac13a0f0
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Delete PTL1/Transcriptomes/Scripts/__pycache__ directory
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2023-10-30 15:18:42 -04:00 |
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Auden Cote-L'Heureux
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e90e177276
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Fixing small oversight in concatenate.py
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2023-10-30 13:00:07 -04:00 |
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Auden Cote-L'Heureux
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6f1c37bcbc
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Updating utils.py to account for addition of concatenation
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2023-10-30 12:49:43 -04:00 |
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Auden Cote-L'Heureux
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2868b53dfc
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Adding concatenation script
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2023-10-30 12:49:12 -04:00 |
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Auden Cote-L'Heureux
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4c4997ecff
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Update CountTaxonOccurence.py
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2023-10-24 11:20:52 -04:00 |
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Auden Cote-L'Heureux
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b3fcdc7c3c
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Update CountTaxonOccurence.py
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2023-10-24 11:20:11 -04:00 |
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Auden Cote-L'Heureux
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81f54d2e1c
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Update and rename CountTreeTips.py to CountTaxonOccurence.py
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2023-10-24 11:19:50 -04:00 |
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Auden Cote-L'Heureux
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9edbf3b87c
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Small fix CountTreeTips.py
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2023-10-24 11:16:11 -04:00 |
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Auden Cote-L'Heureux
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8ae3f7ca57
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Rename count_tips.py to CountTreeTips.py
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2023-10-24 11:15:49 -04:00 |
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Auden Cote-L'Heureux
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9d07bca28c
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Updating arg parsing in tip counting script
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2023-10-24 11:15:37 -04:00 |
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Auden Cote-L'Heureux
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2280edaf5a
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Fixed variable reference error in preguidance.py
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2023-10-21 20:09:27 -04:00 |
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Auden Cote-L'Heureux
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156e4ee8d0
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Removed overlap/dissimilarity filter
(Deleted previous version because of technical GitHub issues)
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2023-10-19 12:49:35 -04:00 |
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Auden Cote-L'Heureux
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f5140c487b
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Delete PTL2/Scripts/preguidance.py
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2023-10-19 12:48:40 -04:00 |
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Auden Cote-L'Heureux
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7169e3666a
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Added OF log to preguidance
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2023-10-15 17:37:43 -04:00 |
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Auden Cote-L'Heureux
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356fc287f0
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Delete PTL2/Scripts/preguidance.py
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2023-10-15 17:37:31 -04:00 |
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Auden Cote-L'Heureux
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7a438d250a
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Small print change in preguidance.py
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2023-10-15 17:25:58 -04:00 |
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Auden Cote-L'Heureux
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7b3860a449
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Update utils.py
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2023-10-13 10:09:16 -04:00 |
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Auden Cote-L'Heureux
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f1d573458b
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Preventing same contig/OG number bug in 4_CountOGsDiamond.py
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2023-10-06 10:42:21 -04:00 |
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Auden Cote-L'Heureux
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a515a08c61
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Fixing same contig/OG number bug in 6_FilterPartials.py
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2023-10-06 10:41:29 -04:00 |
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Auden Cote-L'Heureux
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694ece4648
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Typo
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2023-10-02 12:03:27 -04:00 |
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Auden Cote-L'Heureux
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f4faf95555
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Delete PTL1/Transcriptomes/Scripts/8_SummaryStats.py
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2023-10-02 11:49:27 -04:00 |
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Auden Cote-L'Heureux
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adc96d1dbc
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Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py
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2023-10-02 11:49:20 -04:00 |
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Auden Cote-L'Heureux
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1ee6f5ceb6
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Small changes, see description
- Default partial filter cov threshold is 20%
- Changed script names
- Made requirement of conspecific names file explicit when using XPC
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2023-10-02 11:49:03 -04:00 |
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Auden Cote-L'Heureux
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b2e381e01d
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Typo fix
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2023-10-02 11:12:44 -04:00 |
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Auden Cote-L'Heureux
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4b934b8de2
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Rename 4_InFrameStopCodonEsimator.py to 4_InFrameStopCodonEstimator.py
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2023-10-02 11:11:49 -04:00 |
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Auden Cote-L'Heureux
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fa294909c5
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Updates to script 6 filters & script names
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2023-09-29 13:20:49 -04:00 |
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Auden Cote-L'Heureux
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f9d747ce38
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Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py
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2023-09-29 13:20:17 -04:00 |
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Auden Cote-L'Heureux
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5f28d4447f
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Delete PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py
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2023-09-29 13:20:11 -04:00 |
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Auden Cote-L'Heureux
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eb3db88688
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Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py
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2023-09-29 13:20:05 -04:00 |
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Auden Cote-L'Heureux
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02ec29d737
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Delete PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py
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2023-09-29 13:19:55 -04:00 |
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Auden Cote-L'Heureux
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0b6823d007
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Delete PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py
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2023-09-29 13:19:49 -04:00 |
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Auden Cote-L'Heureux
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6746899daa
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Delete PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py
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2023-09-29 13:19:43 -04:00 |
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Auden Cote-L'Heureux
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18981a792f
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Delete PTL1/Transcriptomes/Scripts/2b_remove_Bact.py
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2023-09-29 13:19:36 -04:00 |
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Auden Cote-L'Heureux
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b6f439e7d6
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Delete PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py
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2023-09-29 13:19:30 -04:00 |
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Auden Cote-L'Heureux
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3e01100304
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Delete PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py
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2023-09-29 13:19:23 -04:00 |
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Auden Cote-L'Heureux
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67bbdd30b8
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Delete PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py
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2023-09-29 13:19:12 -04:00 |
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