adding phylogeny and typing data, large text files are tracked with LFS

ssyamoako · Jul 5, 2022 · e46dec9 · e46dec9
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commit e46dec9
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Showing 42 changed files with 76,281 additions and 40 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/course_data/.DS_Store b/course_data/.DS_Store
diff --git a/course_data/BASH_scripting/dv1_primer.txt b/course_data/BASH_scripting/dv1_primer.txt
@@ -1,40 +1,3 @@
-DENV1_1_LEFT	AGTACAAGAGTCTACGTGGACCGACAAGAA
-DENV1_1_RIGHT	AAACATCGGGCATCAGCATAAGGAGCATGG
-DENV1_2_LEFT	AGTACAAGTGGCTAGATGGGGCTCATTCAA
-DENV1_2_RIGHT	AAACATCGTCGCCAGTTTGGGAACATGTTC
-DENV1_3_LEFT	AGTACAAGGGATTTGGGAGAGTTATGTGAGGAC
-DENV1_3_RIGHT	AAACATCGTCCTGACAGTCCTTCCACGAAG
-DENV1_4_LEFT	AGTACAAGGCACATGCCATAGGAACATCCA
-DENV1_4_RIGHT	AAACATCGACGTTCGTCGACACACAAAGTT
-DENV1_5_LEFT	AGTACAAGTGGACATTGAACTCTTGAAGACGG
-DENV1_5_RIGHT	AAACATCGTGCAGTTGTCCCATGTTCTGTG
-DENV1_6_LEFT	AGTACAAGAGTGTGTGACAAAACTGGAAGGAA
-DENV1_6_RIGHT	AAACATCGTCCTGCTTCTTTGCATGAGCTG
-DENV1_7_LEFT	AGTACAAGTGGCTAGTCCACAAACAATGGTTT
-DENV1_7_RIGHT	AAACATCGCATGGTGCATCTGTTCCTTCGT
-DENV1_8_LEFT	AGTACAAGAGATGGACAAACTGACTCTAAAAGGG
-DENV1_8_RIGHT	AAACATCGTCCAACAGACGTGAACACTCCT
-DENV1_9_LEFT	AGTACAAGAGCTGGTTCAAGAAAGGAAGCA
-DENV1_9_RIGHT	AAACATCGTGCTCTGTCCAAGTGTGAACTT
-DENV1_10_LEFT	AGTACAAGTGCAGTTGGCCTAGTAACGCTA
-DENV1_10_RIGHT	AAACATCGGTTCCATGGGTTGTGGCCTAAT
-DENV1_11_LEFT	AGTACAAGACATCATGTGGAAGCAAATATCAAATGAA
-DENV1_11_RIGHT	AAACATCGTATCCAGTACCCCATGTCAGCG
-DENV1_12_LEFT	AGTACAAGTGGATTTGGAATTTTCACGACAAACA
-DENV1_12_RIGHT	AAACATCGCCGTGGTACCCTCACACAAATC
-DENV1_13_LEFT	AGTACAAGTGATAATTCCAAAGATCTATGGAGGACC
-DENV1_13_RIGHT	AAACATCGGCAGTCCTAGTGAAAAGCTGTCC
-DENV1_14_LEFT	AGTACAAGAGGAGAAGATGGGTGCTGGTAC
-DENV1_14_RIGHT	AAACATCGTCTCTGGATGTTAGTCTGCGGA
-DENV1_15_LEFT	AGTACAAGTATGCATCATGGTTGGAGCCAA
-DENV1_15_RIGHT	AAACATCGTGGACAGGCATAAGGGGAAGAG
-DENV1_16_LEFT	AGTACAAGTGACTGACTTTCAATCACATCAGCT
-DENV1_16_RIGHT	AAACATCGGCTTCTTCTTCCCAGGAGACCT
-DENV1_17_LEFT	AGTACAAGAAAATGATGTGCCGCTAGCTGG
-DENV1_17_RIGHT	AAACATCGACTTCTGGAGGGCTAGGTGTGT
-DENV1_18_LEFT	AGTACAAGCTCTGCTAGCAGTTTCAGGGGT
-DENV1_18_RIGHT	AAACATCGTCTTCTCCCGTGTTCCAGGATC
-DENV1_19_LEFT	AGTACAAGATGTCACCAGGGGAGCTGTACT
-DENV1_19_RIGHT	AAACATCGGCCCTTCTTGTGATGCTTTAGCT
-DENV1_20_LEFT	AGTACAAGTAAACCCGGCACATCTGGATCT
-DENV1_20_RIGHT	AAACATCGTGAAAGTGGCGTGACACATGAG
+version https://git-lfs.github.com/spec/v1
+oid sha256:1b45397a955ce7cb468aa838a7d2cc27d5da0c6940c4ace4df0877d00a1c0434
+size 1875
diff --git a/course_data/phylogeny_typing/.DS_Store b/course_data/phylogeny_typing/.DS_Store
diff --git a/course_data/phylogeny_typing/.gitattributes b/course_data/phylogeny_typing/.gitattributes
@@ -0,0 +1 @@
+*.txt filter=lfs diff=lfs merge=lfs -text
diff --git a/course_data/phylogeny_typing/1_mafft/.DS_Store b/course_data/phylogeny_typing/1_mafft/.DS_Store
diff --git a/course_data/phylogeny_typing/1_mafft/input/reference_sars_cov_2.fas b/course_data/phylogeny_typing/1_mafft/input/reference_sars_cov_2.fas
diff --git a/course_data/phylogeny_typing/1_mafft/input/sars-cov-2.fas b/course_data/phylogeny_typing/1_mafft/input/sars-cov-2.fas
diff --git a/course_data/phylogeny_typing/1_mafft/output/sars-cov-2.aln b/course_data/phylogeny_typing/1_mafft/output/sars-cov-2.aln
diff --git a/course_data/phylogeny_typing/1_mafft/output/sars-cov-2_aln.fas b/course_data/phylogeny_typing/1_mafft/output/sars-cov-2_aln.fas
diff --git a/course_data/phylogeny_typing/2_iqtree/.DS_Store b/course_data/phylogeny_typing/2_iqtree/.DS_Store
diff --git a/course_data/phylogeny_typing/2_iqtree/input/sars-cov-2_aln.fas b/course_data/phylogeny_typing/2_iqtree/input/sars-cov-2_aln.fas
diff --git a/course_data/phylogeny_typing/2_iqtree/output/SARS_new_aln.fas.contree b/course_data/phylogeny_typing/2_iqtree/output/SARS_new_aln.fas.contree
@@ -0,0 +1 @@
+(EPI_ISL_402124:0.0001330601,(((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002340525,(EPI_ISL_6660906_Canada_2021-10-15:0.0010642018,EPI_ISL_6705120_Argentina_2021-10-18:0.0006838218)92:0.0000227862)89:0.0000023304,EPI_ISL_7225062_India_2021-05-11:0.0003759370)92:0.0001054256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100:0.0005722287,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000671219,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001339305,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001958663)75:0.0000020377,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004367673)90:0.0000020377,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003347313)94:0.0000022262)100:0.0006634468,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002007729)100:0.0009280726,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669708,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000672279,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002001809)93:0.0000020299)100:0.0005068280)100:0.0009742769)41:0.0000695819)78:0.0001347954,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)68:0.0000316872,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004370752)62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001992872)70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002700486,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)100:0.0003011544,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002251786,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)97:0.0000748897)90:0.0000025527)100:0.0007059549)77:0.0000643225,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001231856,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0003000514)34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)42:0.0000022119)98:0.0002032259,EPI_ISL_2493026_Angola_2021-03-22:0.0000663902)100:0.0009049323)35:0.0000339823)38:0.0000356907,(1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351353,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691218,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005838205,EPI_ISL_8187166_Colombia_2021-02-19:0.0003675745)82:0.0000020377,EPI_ISL_8564574_Australia_2021-12-31:0.0004345697)96:0.0000353255)62:0.0000020377)100:0.0010222081);
diff --git a/course_data/phylogeny_typing/2_iqtree/output/SARS_new_aln.fas.iqtree b/course_data/phylogeny_typing/2_iqtree/output/SARS_new_aln.fas.iqtree
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		(EPI_ISL_402124:0.0001330601,(((((EPI_ISL_12644861_South_Africa_2021-06-14:0.0002340525,(EPI_ISL_6660906_Canada_2021-10-15:0.0010642018,EPI_ISL_6705120_Argentina_2021-10-18:0.0006838218)92:0.0000227862)89:0.0000023304,EPI_ISL_7225062_India_2021-05-11:0.0003759370)92:0.0001054256,EPI_ISL_8217102_Germany_2021-11-10:0.0000334556)100:0.0005722287,((1ins_29890a-29901a_EPI_ISL_1111130_Peru_2021-01-17:0.0000671219,(((EPI_ISL_1494722_Australia_2021-04-03:0.0001339305,1ins_29734a-29746a_EPI_ISL_2891522_USA_2021-03-12:0.0001958663)75:0.0000020377,EPI_ISL_3824488_Switzerland_2021-08-16:0.0004367673)90:0.0000020377,EPI_ISL_4543939_Sint_Maarten_2021-09-06:0.0003347313)94:0.0000022262)100:0.0006634468,((EPI_ISL_10318197_Denmark_2022-02-15:0.0000020142,EPI_ISL_11528229_Switzerland_2022-03-18:0.0002007729)100:0.0009280726,(EPI_ISL_11680139_Bahamas_2021-12-15:0.0001669708,(EPI_ISL_7834572_Botswana_2021-12-01:0.0000672279,1ins_22155g-22163a_EPI_ISL_9419101_India_2022-01-01:0.0002001809)93:0.0000020299)100:0.0005068280)100:0.0009742769)41:0.0000695819)78:0.0001347954,((((((EPI_ISL_11449404_France_2021-07-17:0.0004015661,EPI_ISL_13025973_Malaysia_2021-05-26:0.0002676869)68:0.0000316872,EPI_ISL_2811956_New_Zealand_2021-06-15:0.0004370752)62:0.0000020142,EPI_ISL_5802461_Brazil_2021-03-07:0.0001992872)70:0.0000334556,EPI_ISL_12388429_Canada_2021-05-27:0.0004015661)100:0.0003680941,(1ins_21931t-21933c_EPI_ISL_1962952_Netherlands_2021-04-18:0.0002700486,((1ins_21989t-21991c_EPI_ISL_4458156_Puerto_Rico_2021-08-30:0.0001672931,1ins_21989t-21991c_EPI_ISL_8482926_Mongolia_2021-07-05:0.0000669128)100:0.0003011544,(1ins_21937t-21939c_EPI_ISL_4984908_Colombia_2021-03-07:0.0002251786,1ins_21967t-21972c_EPI_ISL_8178768_Morocco_2021-07-04:0.0000669128)97:0.0000748897)90:0.0000025527)100:0.0007059549)77:0.0000643225,((1ins_28263a-28266a_EPI_ISL_1197002_Italy_2021-02-10:0.0001231856,((1ins_28200a-28203a_EPI_ISL_2655713_Canada_2021-04-09:0.0002007562,1ins_28215a-28218a_EPI_ISL_4080896_Brazil_2021-07-22:0.0003000514)34:0.0000020142,1ins_28224a-28227a_EPI_ISL_792683_Japan_2021-01-02:0.0000020142)42:0.0000022119)98:0.0002032259,EPI_ISL_2493026_Angola_2021-03-22:0.0000663902)100:0.0009049323)35:0.0000339823)38:0.0000356907,(1ins_25617c-25619c_EPI_ISL_11017424_Jamaica_2021-12-30:0.0004351353,(EPI_ISL_13392375_Ghana_2021-08-10:0.0002691218,((EPI_ISL_13439948_Hong_Kong_2021-10-07:0.0005838205,EPI_ISL_8187166_Colombia_2021-02-19:0.0003675745)82:0.0000020377,EPI_ISL_8564574_Australia_2021-12-31:0.0004345697)96:0.0000353255)62:0.0000020377)100:0.0010222081);