{"id":23057248,"url":"https://github.com/applicativesystem/go-telomeres-graph","last_synced_at":"2025-04-03T05:45:33.665Z","repository":{"id":257927053,"uuid":"872446172","full_name":"applicativesystem/go-telomeres-graph","owner":"applicativesystem","description":"kmer density based telomeres searching and 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go-teleomeres-graph\n\n- searching telomeres across the plant and human genome across tree of life for reassembly of those telomere specific regions. \n- a kmer based approach to search for the matching telomere and then extract the upstream and the downstream of the matching telomere for reassembly of those regions.\n- the tolkit version is present here [tolkit](https://github.com/tolkit/telomeric-identifier), which only plots the kmers and not tell where to look and doesnt provide support for reassembly.\n- the clade specific sets are also present in this repository, which are used in the tolkit for the search. \n- tolkit doesnt allow for the telomere extraction for re-assembly and go-telomeres-graph provide that. \n\n```\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-telomeres-graph ±main⚡ » \\\ngo run main.go -h                                                               \nThis analyzes and reports the telomeres and the corresponding upstream and the downstream from the match telomeres\n\nUsage:\n  telomeres [flags]\n\nFlags:\n  -D, --downstream sequence int         downstream sequence (default 10)\n  -F, --fastaid string                  sequence selection for teleomere (default \"id of the fasta sequence that you want to look for the telomere\")\n  -G, --genome fasta string             fasta genome (default \"genome file in fasta format\")\n  -h, --help                            help for telomeres\n  -I, --kmersize telomere int           telomer kmder define (default 4)\n  -T, --telomere to search for string   teomere search space (default \"string for the telomere\")\n  -U, --upstream sequence int           upstream region for the seqence (default 10)\nexit status 1\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-telomeres-graph ±main⚡ » \ngo run main.go -G fastafile.fasta -F chr10:66478458-66505490 -T ATCGG\nATCGG 33 38\nGCCCAATGAC - upstream\n CGTGTCTAGC - downstream \n GCCCAATGACATCGGCGTGTCTAGC - upstream and downstream with the telomere included\n```\n\n```\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-telomeres-graph ±main⚡ » \n./telomeres -h                                                                  \nThis analyzes and reports the telomeres and the corresponding upstream and the downstream from the match telomeres\n\nUsage:\n  telomeres [flags]\n\nFlags:\n  -D, --downstream sequence int         downstream sequence (default 10)\n  -F, --fastaid string                  sequence selection for teleomere (default \"id of the fasta sequence that you want to look for the telomere\")\n  -G, --genome fasta string             fasta genome (default \"genome file in fasta format\")\n  -h, --help                            help for telomeres\n  -T, --telomere to search for string   teomere search space (default \"string for the telomere\")\n  -U, --upstream sequence int           upstream region for the seqence (default 10)\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-telomeres-graph ±main⚡ » \n./telomeres -G fastafile.fasta -F chr10:66478458-66505490 -T ATCGG\nGCCCAATGAC\n CGTGTCTAGC\n GCCCAATGACATCGGCGTGTCTAGC\n```\n```\nwxr-xr-x. 1 gauavsablok gauavsablok      40 Oct 14 14:58 clades\n-rw-r--r--. 1 gauavsablok gauavsablok      13 Oct 15 13:51 downstream.fasta\n-rwxr-xr-x. 1 gauavsablok gauavsablok     148 Oct 15 11:38 fastafile.fasta\ndrwxr-xr-x. 1 gauavsablok gauavsablok     164 Oct 15 13:51 .git\n-rw-r--r--. 1 gauavsablok gauavsablok     204 Oct 15 09:49 go.mod\n-rw-r--r--. 1 gauavsablok gauavsablok     896 Oct 15 09:49 go.sum\n-rw-r--r--. 1 gauavsablok gauavsablok    4658 Oct 15 13:49 main.go\n-rw-r--r--. 1 gauavsablok gauavsablok    3081 Oct 15 13:53 README.md\n-rw-r--r--. 1 gauavsablok gauavsablok      28 Oct 15 13:51 reassemble.fasta\n-rwxr-xr-x. 1 gauavsablok gauavsablok 5480185 Oct 15 13:51 telomeres\n-rw-r--r--. 1 gauavsablok gauavsablok 5488640 Oct 15 13:52 telomeres.tar\n-rw-r--r--. 1 gauavsablok gauavsablok     161 Oct 15 13:51 telomeres.txt\n-rw-r--r--. 1 gauavsablok gauavsablok      13 Oct 15 13:51 upstream.fasta\n```\nGaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Fgo-telomeres-graph","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fapplicativesystem%2Fgo-telomeres-graph","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Fgo-telomeres-graph/lists"}