v1.0.0 -> v1.1.0

CHANGELOG.md

@@ -0,0 +1,21 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [1.1.0] - 2022-08-22
+### Added
+- Support for random-gamete-based recombination analysis (key feature enhancement).
+- Add a few new auxiliary scripts to prepare for future updates.
+### Changed
+- Enable a Better handling for generating per-marker-based parental allele freqeuncy summary files and the associated plots.
+- Update the version of SRAtools to v3.0.0 to cope with the change from the remote end of NCBI's SRA database.
+- Update the Manual.
+### Fixed
+- Typos in the Manual.
+
+## [1.0.0] - 2022-05-07
+### Added
+- Initial version of RecombineX.

Example_Outputs/02.Polymorphic_Markers_by_Reference_based_Read_Mapping/S288C-SK1.ref.final.SNP.markers.intermarker_distance.txt

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+prefix	marker_count	mean_distance	median_distance	stdev_distance
+S288C-SK1.ref.final.SNP.markers	58668	202.04	102.00	436.49

Example_Outputs/03.Gamete_Read_Mapping_to_Reference_Genome/all_samples.coverage_summary.txt

@@ -0,0 +1,21 @@
+sample	ref_genome	total_reads	mapping_rate	pairing_rate	(>=5)_depth_proportion	zero_depth_proportion	mean_depth	median_depth	ref_chrI_mean_depth	ref_chrI_median_depth	ref_chrII_mean_depth	ref_chrII_median_depth	ref_chrIII_mean_depth	ref_chrIII_median_depth	ref_chrIV_mean_depth	ref_chrIV_median_depth	ref_chrV_mean_depth	ref_chrV_median_depth	ref_chrVI_mean_depth	ref_chrVI_median_depth	ref_chrVII_mean_depth	ref_chrVII_median_depth	ref_chrVIII_mean_depth	ref_chrVIII_median_depth	ref_chrIX_mean_depth	ref_chrIX_median_depth	ref_chrX_mean_depth	ref_chrX_median_depth	ref_chrXI_mean_depth	ref_chrXI_median_depth	ref_chrXII_mean_depth	ref_chrXII_median_depth	ref_chrXIII_mean_depth	ref_chrXIII_median_depth	ref_chrXIV_mean_depth	ref_chrXIV_median_depth	ref_chrXV_mean_depth	ref_chrXV_median_depth	ref_chrXVI_mean_depth	ref_chrXVI_median_depth
+AND1702-8.a	ref.genome.fa	9921462	1.00	1.00	0.95	0.04	80.29	83.00	71.20	84.00	82.23	85.00	84.63	88.00	79.58	82.00	80.80	84.00	87.82	91.00	79.31	83.00	81.68	85.00	82.77	86.00	80.01	85.00	83.99	86.00	77.89	80.00	80.09	83.00	81.44	85.00	78.18	82.00	79.21	82.00
+AND1702-8.b	ref.genome.fa	12601368	1.00	1.00	0.95	0.04	102.14	107.00	113.58	121.00	104.07	109.00	112.34	116.00	97.89	104.00	103.22	109.00	116.01	120.00	102.03	106.00	100.14	108.00	101.06	108.00	100.66	108.00	108.49	111.00	96.03	100.00	102.67	107.00	102.33	108.00	104.62	106.00	98.44	105.00
+AND1702-8.c	ref.genome.fa	12369584	1.00	1.00	0.95	0.04	100.19	105.00	85.94	101.00	100.92	106.00	108.42	110.00	96.75	103.00	100.59	107.00	103.97	111.00	99.67	105.00	98.93	105.00	99.06	106.00	99.25	106.00	105.72	108.00	99.65	104.00	101.84	106.00	102.16	107.00	102.23	105.00	98.25	104.00
+AND1702-8.d	ref.genome.fa	11426588	1.00	1.00	0.95	0.04	92.49	97.00	96.55	103.00	96.14	100.00	90.98	98.00	89.53	95.00	93.87	99.00	95.43	102.00	93.01	97.00	90.80	97.00	92.11	99.00	93.69	99.00	98.03	101.00	90.19	94.00	94.42	99.00	95.22	99.00	89.86	95.00	89.21	96.00
+AND1702-9.a	ref.genome.fa	12630440	1.00	1.00	0.95	0.04	102.22	107.00	108.14	117.00	104.20	108.00	106.32	112.00	97.79	103.00	105.11	110.00	109.10	115.00	102.99	107.00	100.40	107.00	104.20	110.00	101.54	108.00	105.26	108.00	100.98	103.00	103.16	107.00	103.87	108.00	99.83	105.00	100.70	105.00
+AND1702-9.b	ref.genome.fa	12000479	1.00	1.00	0.95	0.04	97.36	102.00	86.70	102.00	100.14	104.00	104.77	109.00	94.41	99.00	99.58	105.00	106.96	112.00	95.65	101.00	96.77	103.00	94.23	102.00	96.85	104.00	102.78	106.00	95.46	99.00	99.22	103.00	98.67	104.00	97.45	101.00	95.28	101.00
+AND1702-9.c	ref.genome.fa	11511160	1.00	1.00	0.95	0.05	93.39	97.00	96.30	113.00	94.84	98.00	109.90	112.00	87.25	92.00	96.27	100.00	105.06	111.00	90.57	95.00	93.58	98.00	98.48	103.00	94.45	99.00	101.11	102.00	87.85	91.00	95.11	97.00	94.08	97.00	94.25	95.00	88.33	93.00
+AND1702-9.d	ref.genome.fa	6920088	1.00	1.00	0.96	0.04	54.31	52.00	63.66	58.00	53.40	52.00	61.05	57.00	51.76	50.00	56.50	53.00	63.08	56.00	54.52	52.00	51.10	50.00	54.80	54.00	51.37	50.00	56.18	52.00	56.52	51.00	54.05	52.00	53.49	52.00	54.48	51.00	51.49	50.00
+AND1702-10.a	ref.genome.fa	8342886	1.00	1.00	0.95	0.04	67.74	70.00	64.54	75.00	70.08	71.00	71.22	74.00	64.96	68.00	68.65	71.00	74.35	78.00	66.62	69.00	67.53	71.00	70.08	73.00	67.12	71.00	71.89	73.00	65.80	67.00	68.75	71.00	67.84	70.00	68.01	70.00	66.06	69.00
+AND1702-10.b	ref.genome.fa	11413564	1.00	1.00	0.95	0.05	92.59	97.00	96.07	105.00	95.09	99.00	101.35	105.00	88.99	94.00	95.41	100.00	99.70	105.00	91.97	96.00	89.31	96.00	90.81	98.00	91.54	97.00	96.88	99.00	90.39	93.00	92.82	97.00	93.35	98.00	92.70	96.00	91.55	96.00
+AND1702-10.c	ref.genome.fa	11051551	1.00	1.00	0.95	0.04	89.68	93.00	102.60	110.00	90.56	94.00	102.29	102.00	85.46	90.00	92.54	96.00	102.51	106.00	88.57	92.00	89.20	94.00	87.93	93.00	90.08	94.00	95.61	96.00	85.54	88.00	89.86	93.00	91.46	94.00	88.70	91.00	85.10	90.00
+AND1702-10.d	ref.genome.fa	11681948	1.00	1.00	0.95	0.04	94.84	99.00	86.96	101.00	95.83	100.00	98.97	104.00	90.79	97.00	95.30	101.00	103.47	108.00	95.34	99.00	96.88	101.00	99.26	104.00	92.94	99.00	100.47	103.00	93.08	97.00	96.43	100.00	97.43	101.00	94.29	98.00	90.91	97.00
+AND1702-11.a	ref.genome.fa	12316531	1.00	1.00	0.95	0.04	100.12	105.00	106.50	117.00	101.35	106.00	112.88	114.00	95.45	101.00	102.76	108.00	113.19	118.00	99.88	104.00	98.19	104.00	96.74	105.00	99.75	106.00	105.29	108.00	96.33	100.00	100.11	104.00	100.68	105.00	101.44	103.00	97.52	103.00
+AND1702-11.b	ref.genome.fa	8576307	1.00	1.00	0.95	0.04	69.62	72.00	73.03	79.00	70.66	73.00	75.52	79.00	66.29	70.00	71.04	74.00	76.41	80.00	68.12	71.00	69.69	73.00	72.59	75.00	70.11	73.00	74.68	75.00	68.72	70.00	70.53	72.00	69.00	72.00	67.48	71.00	67.97	71.00
+AND1702-11.c	ref.genome.fa	9746801	1.00	1.00	0.95	0.05	79.18	83.00	72.07	84.00	79.64	82.00	81.90	86.00	76.72	81.00	78.95	83.00	84.46	89.00	78.88	82.00	78.15	83.00	81.56	84.00	78.64	83.00	83.90	85.00	78.00	81.00	80.55	83.00	81.47	84.00	80.00	82.00	76.38	81.00
+AND1702-11.d	ref.genome.fa	12767783	1.00	1.00	0.95	0.04	103.80	109.00	102.30	118.00	107.28	111.00	111.69	118.00	98.89	105.00	108.22	113.00	112.48	119.00	105.10	110.00	103.75	110.00	103.33	112.00	103.25	110.00	108.87	112.00	99.49	103.00	105.16	110.00	105.83	111.00	103.23	107.00	99.51	106.00
+AND1702-12.a	ref.genome.fa	7670287	1.00	1.00	0.95	0.04	62.23	64.00	70.83	77.00	63.12	65.00	72.08	72.00	58.42	61.00	63.04	65.00	84.03	81.00	61.12	63.00	62.50	65.00	63.25	65.00	61.64	64.00	65.56	66.00	58.81	60.00	61.64	63.00	63.38	65.00	61.30	62.00	58.91	62.00
+AND1702-12.b	ref.genome.fa	12335897	1.00	1.00	0.95	0.04	100.30	105.00	113.88	121.00	102.19	106.00	103.86	111.00	95.33	101.00	103.57	107.00	108.55	115.00	101.13	104.00	97.78	105.00	100.49	107.00	99.46	105.00	104.98	107.00	97.73	101.00	101.65	105.00	102.12	106.00	100.15	103.00	95.93	102.00
+AND1702-12.c	ref.genome.fa	12346215	1.00	1.00	0.95	0.04	100.39	106.00	91.69	107.00	101.63	106.00	106.51	112.00	97.44	103.00	102.08	107.00	105.19	112.00	98.69	105.00	101.33	106.00	103.66	109.00	100.58	107.00	106.96	109.00	98.13	103.00	101.39	106.00	102.12	107.00	98.86	104.00	98.81	104.00
+AND1702-12.d	ref.genome.fa	12741714	1.00	1.00	0.95	0.04	103.46	109.00	96.67	113.00	106.10	110.00	110.34	115.00	99.72	106.00	103.35	110.00	114.77	120.00	103.17	108.00	102.97	109.00	105.39	111.00	102.57	110.00	110.08	113.00	100.11	105.00	105.42	110.00	104.29	110.00	103.60	107.00	100.22	106.00

Example_Outputs/12.Polymorphic_Markers_by_Cross_Parent_Genome_Alignment/S288C-SK1.S288C.final.SNP.markers.intermarker_distance.txt

@@ -0,0 +1,2 @@
+prefix	marker_count	mean_distance	median_distance	stdev_distance
+S288C-SK1.S288C.final.SNP.markers	60506	197.56	96.00	450.60

Example_Outputs/12.Polymorphic_Markers_by_Cross_Parent_Genome_Alignment/S288C-SK1.SK1.final.SNP.markers.intermarker_distance.txt

@@ -0,0 +1,2 @@
+prefix	marker_count	mean_distance	median_distance	stdev_distance
+S288C-SK1.SK1.final.SNP.markers	60506	194.64	96.00	416.73

Example_Outputs/14.Polymorphic_Markers_by_Consensus/S288C-SK1.S288C.final.SNP.markers.intermarker_distance.txt

@@ -0,0 +1,2 @@
+prefix	marker_count	mean_distance	median_distance	stdev_distance
+S288C-SK1.S288C.final.SNP.markers	48672	240.37	120.00	521.91

Example_Outputs/14.Polymorphic_Markers_by_Consensus/S288C-SK1.SK1.final.SNP.markers.intermarker_distance.txt

@@ -0,0 +1,2 @@
+prefix	marker_count	mean_distance	median_distance	stdev_distance
+S288C-SK1.SK1.final.SNP.markers	48672	235.91	120.00	444.11