{"action":"created","issue":{"url":"https://api.github.com/repos/SaraEl-Metwally/LightAssembler/issues/4","repository_url":"https://api.github.com/repos/SaraEl-Metwally/LightAssembler","labels_url":"https://api.github.com/repos/SaraEl-Metwally/LightAssembler/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/SaraEl-Metwally/LightAssembler/issues/4/comments","events_url":"https://api.github.com/repos/SaraEl-Metwally/LightAssembler/issues/4/events","html_url":"https://github.com/SaraEl-Metwally/LightAssembler/issues/4","id":175662605,"number":4,"title":"Link to example data: ecoli_reads_1.fq ecoli_reads_2.fq","user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-09-08T04:29:14Z","updated_at":"2016-09-30T10:17:46Z","closed_at":null,"body":"Where can we get the `ecoli_reads_1.fq ecoli_reads_2.fq` files to replicate your examples?\r\n\r\nEvery time I try on my own `fastq.gz` data I get this message:\r\n\r\n```\r\n--- Parameters extrapolation.\r\n\r\n--- h(0):m(0):s(8) elapsed time.\r\n--- start with gap size g = 8\r\n--- average read length = 137\r\n--- average sequencing coverage = 131\r\n\r\n--- Uniform kmers sampling.\r\n\r\n--- h(0):m(0):s(0) elapsed time.\r\n--- total number of kmers in BloomA = 0\r\n--- BloomA false positive rate = 0\r\n--- probability of an incorrect kmer appears in the sample : 0.151046\r\n\r\n--- Trusted/untrusted kmers filtering.\r\n\r\n--- h(0):m(0):s(0) elapsed time.\r\n--- total number of kmers in BloomB = 0\r\n--- BloomB false positive rate = 0\r\n--- LightAssembler can not assemble your dataset !!!\r\n--- maximum supported read length for this version = 1024\r\n--- try different values for k [kmer size] & g [gap size] or different dataset\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/SaraEl-Metwally/LightAssembler/issues/comments/250710354","html_url":"https://github.com/SaraEl-Metwally/LightAssembler/issues/4#issuecomment-250710354","issue_url":"https://api.github.com/repos/SaraEl-Metwally/LightAssembler/issues/4","id":250710354,"user":{"login":"SaraEl-Metwally","id":16980331,"avatar_url":"https://avatars.githubusercontent.com/u/16980331?v=3","gravatar_id":"","url":"https://api.github.com/users/SaraEl-Metwally","html_url":"https://github.com/SaraEl-Metwally","followers_url":"https://api.github.com/users/SaraEl-Metwally/followers","following_url":"https://api.github.com/users/SaraEl-Metwally/following{/other_user}","gists_url":"https://api.github.com/users/SaraEl-Metwally/gists{/gist_id}","starred_url":"https://api.github.com/users/SaraEl-Metwally/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SaraEl-Metwally/subscriptions","organizations_url":"https://api.github.com/users/SaraEl-Metwally/orgs","repos_url":"https://api.github.com/users/SaraEl-Metwally/repos","events_url":"https://api.github.com/users/SaraEl-Metwally/events{/privacy}","received_events_url":"https://api.github.com/users/SaraEl-Metwally/received_events","type":"User","site_admin":false},"created_at":"2016-09-30T10:17:46Z","updated_at":"2016-09-30T10:17:46Z","body":"- We simulated ten different data sets from [**E. coli reference genome** ] (https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2) using  [**Mason** v0.1.2] (https://packages.seqan.de/mason/), these data sets are varying in coverage (25x,35x,75x,140x,and 280x) and average error rate (1% and 3%).  \r\n\r\n- You can also replicate our results using real benchmark data sets from [**GAGE**] (http://gage.cbcb.umd.edu/data/index.html)  and [**Assemblathon bird data set**] (https://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=ERX218680)\r\n\r\n- The exact command lines used for the simulated and real data sets can be found in the supplementary file attached with [**LightAssembler**](http://bioinformatics.oxfordjournals.org/content/early/2016/07/27/bioinformatics.btw470.abstract) paper."}}
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