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https://github.com/fjruizruano/ngs-protocols
05 April 2024, 22:19:15 UTC
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Revision Author Date Message Commit Date
39a091d fjruizruano 03 August 2023, 11:48:27 UTC adding gfa2fas.py and extract_gfa.py 03 August 2023, 11:48:27 UTC
ccdbd0a fjruizruano 01 September 2022, 19:19:18 UTC adding get_coordinates 01 September 2022, 19:19:18 UTC
869b03c fjruizruano 27 July 2022, 07:05:13 UTC Adding novoplasty_run.py 27 July 2022, 07:05:13 UTC
fe96fc5 fjruizruano 27 July 2022, 05:40:30 UTC adding mapping_blat_gs_nonormal.py 27 July 2022, 05:40:30 UTC
0524589 fjruizruano 16 November 2021, 00:51:38 UTC adding ssaha2_run_multi_id99_len80.py 16 November 2021, 00:51:38 UTC
671568d fjruizruano 16 November 2021, 00:47:35 UTC updating extract_barcoded_reads_from_bam.py 16 November 2021, 00:47:35 UTC
ca66488 fjruizruano 21 July 2021, 22:23:05 UTC updating repeat_masker_run_big to join out files and clean splits 21 July 2021, 22:23:05 UTC
70110b3 fjruizruano 30 June 2021, 14:59:42 UTC *solving a bug* 30 June 2021, 14:59:42 UTC
242e65d fjruizruano 29 June 2021, 00:19:41 UTC report matches in rm_homology_v2.py 29 June 2021, 00:19:41 UTC
3db2ac6 fjruizruano 29 June 2021, 00:11:47 UTC report matches in rm_homology_v2.py 29 June 2021, 00:11:47 UTC
e14c7d7 fjruizruano 29 June 2021, 00:05:27 UTC report matches in rm_homology_v2.py 29 June 2021, 00:05:27 UTC
dd4d253 fjruizruano 29 June 2021, 00:00:23 UTC rm_homology_v2.py without output file 29 June 2021, 00:00:23 UTC
3254836 fjruizruano 28 June 2021, 23:51:07 UTC adding rm_homology_v2.py 28 June 2021, 23:51:07 UTC
b924ac5 fjruizruano 18 June 2021, 22:24:44 UTC adding cds detection for truncation in coverage_graphics 18 June 2021, 22:24:44 UTC
31720b1 fjruizruano 18 June 2021, 19:24:51 UTC adding truncation test in coverage_graphics 18 June 2021, 19:24:51 UTC
a05a48a fjruizruano 27 May 2021, 21:12:43 UTC Adding get_shared_pw_shared_sunks.py 27 May 2021, 21:12:43 UTC
45efac9 Paquillo 26 March 2021, 01:36:31 UTC updating count_reads_bam.py 26 March 2021, 01:36:31 UTC
09d12f8 Paquillo 11 February 2021, 22:58:53 UTC adding rm_getseq_stats.py 11 February 2021, 22:58:53 UTC
a948c24 Paquillo 13 January 2021, 22:17:56 UTC updating divnuc_bam.py 13 January 2021, 22:17:56 UTC
c095c0a Paquillo 18 November 2020, 01:36:22 UTC bwa_mem_protocol.py 18 November 2020, 01:36:22 UTC
89da5f5 Paquillo 18 November 2020, 00:11:02 UTC Merge branch 'master' of https://github.com/fjruizruano/ngs-protocols 18 November 2020, 00:11:02 UTC
51af7a8 Paquillo 18 November 2020, 00:10:06 UTC updating bowtie2_protocol.py 18 November 2020, 00:10:06 UTC
da41c4d Francisco J. Ruiz-Ruano 01 September 2020, 21:51:34 UTC Merge pull request #6 from MilanCalegari/patch-1 New input and output option to rm_join_out.py 01 September 2020, 21:51:34 UTC
17cd8a3 Rodrigo Milan Calegari 29 August 2020, 23:10:25 UTC New input and output option to rm_join_out.py With this changes is not mandatory to use "lista_out.txt" as input and "test.all.out" as output. If you run the script with no options, it will run as before but with this changes you can pass the names of input and output example: rm_join_out.py input.out output.out 29 August 2020, 23:10:25 UTC
15cacde Paquillo 21 July 2020, 16:52:57 UTC adding raxml_protocol.py 21 July 2020, 16:52:57 UTC
a9fd879 Paquillo 15 July 2020, 21:41:15 UTC Adding sat_cross_libraries.py 15 July 2020, 21:41:15 UTC
7e7618c Paquillo 06 July 2020, 15:51:41 UTC adding rexp_get_contigs_re2 06 July 2020, 15:51:41 UTC
51b2059 Paquillo 22 June 2020, 20:18:13 UTC Updated get_var_library 22 June 2020, 20:18:13 UTC
360f282 Paquillo 18 June 2020, 03:30:46 UTC weigthened average in divsum_stats 18 June 2020, 03:30:46 UTC
1fc5b0f Paquillo 18 June 2020, 03:04:18 UTC adding divsum_stats.py 18 June 2020, 03:04:18 UTC
dbcad90 Paquillo 12 May 2020, 02:39:01 UTC updating peru_protocol.py 12 May 2020, 02:39:01 UTC
f40fc60 fjruizruano 24 April 2020, 02:22:19 UTC Updating peru_protocol.py 24 April 2020, 02:22:19 UTC
c116417 fjruizruano 24 April 2020, 02:14:06 UTC Updating peru_protocol.py 24 April 2020, 02:14:06 UTC
a9f4f43 fjruizruano 24 April 2020, 02:12:32 UTC rm_count_matches_monomers.py 24 April 2020, 02:12:32 UTC
d56748c fjruizruano 24 April 2020, 02:01:19 UTC rm_cluster_external.py 24 April 2020, 02:01:19 UTC
10296f2 fjruizruano 23 April 2020, 23:32:47 UTC Adding PERU protocol 23 April 2020, 23:32:47 UTC
1b77f70 fjruizruano 13 April 2020, 19:08:28 UTC updating rexp_get_cluster 13 April 2020, 19:08:28 UTC
2b687c8 fjruizruano 13 April 2020, 19:07:10 UTC updating rexp_get_cluster 13 April 2020, 19:07:10 UTC
071e05d fjruizruano 13 April 2020, 17:16:05 UTC adding divsum_join_annot 13 April 2020, 17:16:05 UTC
08dc437 fjruizruano 13 April 2020, 16:43:16 UTC adding rexp_annot.py 13 April 2020, 16:43:16 UTC
a32d013 fjruizruano 22 February 2020, 16:54:48 UTC updating ssaha2_run_multi.py 22 February 2020, 16:54:48 UTC
a8648ad fjruizruano 20 February 2020, 09:12:37 UTC Resolving bug with samtools versions in ssaha2_run_multi.py 20 February 2020, 09:12:37 UTC
d009baf fjruizruano 18 February 2020, 14:48:46 UTC update ssha2_run_multi.py 18 February 2020, 14:48:46 UTC
5a21081 fjruizruano 14 December 2019, 20:31:42 UTC longranger_prepare_reference.py 14 December 2019, 20:31:42 UTC
f1cee91 fjruizruano 19 November 2019, 14:59:39 UTC Adding alignment_copy_paste.py 19 November 2019, 14:59:39 UTC
892e729 fjruizruano 19 November 2019, 14:56:31 UTC Adding align_copy_paste.py 19 November 2019, 14:56:31 UTC
de06b12 fjruizruano 28 October 2019, 14:43:29 UTC updating readme 28 October 2019, 14:43:29 UTC
59d4b5f fjruizruano 28 October 2019, 14:42:13 UTC adding repeat_landscape_decimal_050 28 October 2019, 14:42:13 UTC
56acecf fjruizruano 13 October 2019, 23:59:29 UTC updating repeat_landscape_decimal.py 13 October 2019, 23:59:29 UTC
25c5607 fjruizruano 13 October 2019, 23:41:27 UTC updating repeat_landscape_decimal.py 13 October 2019, 23:41:27 UTC
0c4e270 fjruizruano 13 October 2019, 23:37:49 UTC repeat_landscape_decimal.py 13 October 2019, 23:37:49 UTC
4c71b61 fjruizruano 03 October 2019, 08:03:15 UTC adding gff_creator.py 03 October 2019, 08:03:15 UTC
efefe17 fjruizruano 09 August 2019, 22:10:26 UTC adding get_var_library.py 09 August 2019, 22:10:26 UTC
bf44a07 fjruizruano 06 January 2019, 03:27:59 UTC updating extract_barcoded 06 January 2019, 03:27:59 UTC
58df8a0 fjruizruano 06 January 2019, 03:14:52 UTC updating extract_barcoded 06 January 2019, 03:14:52 UTC
dce7dbe fjruizruano 06 January 2019, 02:36:03 UTC updating extract_barcoded 06 January 2019, 02:36:03 UTC
cd5013d fjruizruano 05 January 2019, 15:59:08 UTC adding extract_barcoded_reads_from_bam.py 05 January 2019, 15:59:08 UTC
b4dec9b fjruizruano 05 January 2019, 15:56:46 UTC Updating ssaha2_run_multi*.py 05 January 2019, 15:56:46 UTC
897c819 fjruizruano 05 January 2019, 15:53:44 UTC Updating ssaha2_run_multi.py 05 January 2019, 15:53:44 UTC
a6a635c fjruizruano 19 November 2018, 14:07:48 UTC only high coverage regions in coverage_graphics.py 19 November 2018, 14:07:48 UTC
5549287 fjruizruano 16 November 2018, 12:30:52 UTC coverage_graphics.py with improved hig/low coverage support 16 November 2018, 12:30:52 UTC
e06e0be fjruizruano 16 November 2018, 10:08:06 UTC coverage_graphics.py with improved hig/low coverage support 16 November 2018, 10:08:06 UTC
1aeadc3 fjruizruano 15 November 2018, 19:04:41 UTC coverage_graphics.py with hig/low coverrage support 15 November 2018, 19:04:41 UTC
4a09ac6 fjruizruano 15 November 2018, 17:30:08 UTC coverage_graphics.py with primer support 15 November 2018, 17:30:08 UTC
ab917b1 fjruizruano 15 November 2018, 14:59:01 UTC big update of coverage_graphics.py with CDS and SNPs support 15 November 2018, 14:59:01 UTC
60c3926 fjruizruano 15 November 2018, 12:20:33 UTC big update of coverage_graphics.py with CDS and SNPs support 15 November 2018, 12:20:33 UTC
5acdda2 fjruizruano 05 October 2018, 19:53:17 UTC updating massive_phylogeny.py 05 October 2018, 19:53:17 UTC
98b3fcf fjruizruano 05 October 2018, 16:40:54 UTC updatind coverage_graphics_coord.py 05 October 2018, 16:40:54 UTC
24b4477 fjruizruano 05 October 2018, 15:52:07 UTC update coverage_graphics_coord 05 October 2018, 15:52:07 UTC
26aab29 fjruizruano 04 October 2018, 22:03:50 UTC adding coverage_graphics_coord 04 October 2018, 22:03:50 UTC
e04a507 fjruizruano 19 September 2018, 17:06:59 UTC adding massive_phylogenies_figure.py 19 September 2018, 17:06:59 UTC
5a11b96 fjruizruano 19 September 2018, 15:21:59 UTC adding massive_phylogeny 19 September 2018, 15:21:59 UTC
fb0d7b5 fjruizruano 17 September 2018, 19:55:03 UTC updating reduce_bam 17 September 2018, 19:55:03 UTC
4a77afe fjruizruano 16 August 2018, 10:24:09 UTC updating bwa_protocol.py 16 August 2018, 10:24:09 UTC
9ff5aab fjruizruano 11 August 2018, 15:41:25 UTC adding snp_calling_bchr_z10.py 11 August 2018, 15:41:25 UTC
2aa0557 fjruizruano 28 June 2018, 22:09:18 UTC adding dimerator.py 28 June 2018, 22:09:18 UTC
520d74e fjruizruano 28 June 2018, 16:19:41 UTC updating satminer_quant script 28 June 2018, 16:19:41 UTC
5ae43d6 fjruizruano 28 June 2018, 14:08:34 UTC adding satminer_quant and divsum_ab 28 June 2018, 14:08:34 UTC
04fea45 fjruizruano 28 June 2018, 14:06:18 UTC updating divsum_to_rl.py 28 June 2018, 14:06:18 UTC
2599861 fjruizruano 28 June 2018, 09:23:36 UTC adding replace_patterns.py 28 June 2018, 09:23:36 UTC
41ce399 fjruizruano 22 June 2018, 18:11:33 UTC divsum_to_rl.py with substractive rl support 22 June 2018, 18:11:33 UTC
3988758 fjruizruano 22 June 2018, 12:07:43 UTC Adding divsum_to_rl.py 22 June 2018, 12:07:43 UTC
f2c8967 fjruizruano 02 June 2018, 17:20:21 UTC updating cd_hit_filter_size 02 June 2018, 17:20:21 UTC
7ae848f fjruizruano 02 June 2018, 14:59:28 UTC updating cd_hit_filter_size.py 02 June 2018, 14:59:28 UTC
f375cfe fjruizruano 02 June 2018, 14:24:17 UTC Adding cd_hit_filter_size.py 02 June 2018, 14:24:17 UTC
9507279 fjruizruano 30 May 2018, 19:02:23 UTC updating bam_consensus.py 30 May 2018, 19:02:23 UTC
05c2018 fjruizruano 24 May 2018, 22:43:57 UTC adding read counter to count_bases_fastq.py 24 May 2018, 22:43:57 UTC
1a4df2c fjruizruano 17 May 2018, 02:48:58 UTC updating sequence_ref_alt.py 17 May 2018, 02:48:58 UTC
a096bd2 fjruizruano 11 May 2018, 00:14:27 UTC improving bam_var_join.py 11 May 2018, 00:14:27 UTC
42cb529 fjruizruano 10 May 2018, 23:42:09 UTC solving bug in snp_caling_bchr 10 May 2018, 23:42:09 UTC
6c3c041 fjruizruano 04 May 2018, 22:30:12 UTC adding annot_to_rexp.py 04 May 2018, 22:30:12 UTC
14d1b7e fjruizruano 03 May 2018, 18:19:03 UTC bam_coverage_join.py bug 03 May 2018, 18:19:03 UTC
909501f fjruizruano 03 May 2018, 15:21:01 UTC bam_coverage_join.py recognizes var files 03 May 2018, 15:21:01 UTC
bbccebb fjruizruano 03 May 2018, 03:41:46 UTC updating rm_getseq_split.py 03 May 2018, 03:41:46 UTC
3e771d9 fjruizruano 02 May 2018, 23:37:24 UTC updating rm_getseq_split.py 02 May 2018, 23:37:24 UTC
7548eb0 fjruizruano 02 May 2018, 23:14:53 UTC updating rm_getseq_split.py 02 May 2018, 23:14:53 UTC
5d53d4f fjruizruano 02 May 2018, 23:07:05 UTC updating rm_getseq_split.py 02 May 2018, 23:07:05 UTC
f47f25b fjruizruano 02 May 2018, 22:40:20 UTC adding rm_getseq_split.py 02 May 2018, 22:40:20 UTC
d02033e fjruizruano 02 May 2018, 20:13:26 UTC Solving a bug in coverage_graphics.py 02 May 2018, 20:13:26 UTC
45ea781 fjruizruano 23 April 2018, 15:40:00 UTC adding trinity_extract_longest2.py 23 April 2018, 15:40:00 UTC
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