{"__v":4,"_id":"57619028b65324200072d6c6","api":{"auth":"required","params":[],"results":{"codes":[]},"settings":"","url":""},"body":">**Once we were blobs in the sea...**\n>\n>-*Terry Pratchett, A Hat Full of Sky*\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"General description\"\n}\n[/block]\nBlobtools is a tool set for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots [Kumar et al. 2012](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843372/pdf/fgene-04-00237.pdf).\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"What can I do with blobtools?\"\n}\n[/block]\n```blobtools``` consist of a series of tools that can be used to \n* collate information associated with an assembly file, such as:\n * sequence ID\n * sequence length\n * GC-content\n * coverage information\n * taxonomy information (sequence similarity search hits)\n * user-defined categories\n* visualise information using blobplots, covplots and/or readcovplots.\n* extract information into human- and computer-readable files\n* produce paper-ready figures\n\nUse cases include:\n* *de-novo* genome projects\n * visualisation of the assembly\n * identification of target genome, associated biota, contaminants, ...\n * informing [Read-filtering strategies](doc:read-filtering-strategies) \n* genome resequencing projects \n * visualisation of the assembly\n * identification of \"core\" genome, \"pan\" genome, associated biota, contaminants, ...\n * identification of target genome, associated biota, contaminants, ...\n * informing [Read-filtering strategies](doc:read-filtering-strategies) \n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"What tools are included in blobtools?\"\n}\n[/block]\n* ```blobtools create``` can create a blobDB by parsing information from \n * one [assembly file](doc:assembly-file)\n * one (or more) [coverage file(s)](doc:coverage-file)\n * one (or more) [taxonomy file(s)](doc:taxonomy-file)\n * one [nodesDB file](doc:taxonomy-database)\n\n\n*  ```blobtools view``` can extract information from a blobDB \n\n\n* ```blobtools blobplot``` can visualise information from a blobDB in a blobplot\n\n\n* ```blobtools covplot``` can visualise information from a blobDB in a covplot\n\n\n* ```blobtools map2cov``` can generate a [COV file](doc:coverage-file) from one or more BAM/SAM/CAS file(s)\n\n\n* ```blobtools seqfilter``` can filter FASTA files based on a list of sequence names\n\n\n* ```blobtools taxify``` can annotate \"taxid\" field in Taxonomy files by using a TAXID file","category":"57618347b65324200072d6a9","createdAt":"2016-06-15T17:28:08.942Z","excerpt":"","githubsync":"","hidden":false,"isReference":false,"link_external":false,"link_url":"","order":0,"parentDoc":null,"project":"57618347b65324200072d6a5","slug":"what-is-blobtools","sync_unique":"","title":"blobtools","type":"basic","updates":[],"user":"57617c8caa540f3600bfed20","version":"57618347b65324200072d6a8","childrenPages":[]}
>**Once we were blobs in the sea...** > >-*Terry Pratchett, A Hat Full of Sky* [block:api-header] { "type": "basic", "title": "General description" } [/block] Blobtools is a tool set for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots [Kumar et al. 2012](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843372/pdf/fgene-04-00237.pdf). [block:api-header] { "type": "basic", "title": "What can I do with blobtools?" } [/block] ```blobtools``` consist of a series of tools that can be used to * collate information associated with an assembly file, such as: * sequence ID * sequence length * GC-content * coverage information * taxonomy information (sequence similarity search hits) * user-defined categories * visualise information using blobplots, covplots and/or readcovplots. * extract information into human- and computer-readable files * produce paper-ready figures Use cases include: * *de-novo* genome projects * visualisation of the assembly * identification of target genome, associated biota, contaminants, ... * informing [Read-filtering strategies](doc:read-filtering-strategies) * genome resequencing projects * visualisation of the assembly * identification of "core" genome, "pan" genome, associated biota, contaminants, ... * identification of target genome, associated biota, contaminants, ... * informing [Read-filtering strategies](doc:read-filtering-strategies) [block:api-header] { "type": "basic", "title": "What tools are included in blobtools?" } [/block] * ```blobtools create``` can create a blobDB by parsing information from * one [assembly file](doc:assembly-file) * one (or more) [coverage file(s)](doc:coverage-file) * one (or more) [taxonomy file(s)](doc:taxonomy-file) * one [nodesDB file](doc:taxonomy-database) * ```blobtools view``` can extract information from a blobDB * ```blobtools blobplot``` can visualise information from a blobDB in a blobplot * ```blobtools covplot``` can visualise information from a blobDB in a covplot * ```blobtools map2cov``` can generate a [COV file](doc:coverage-file) from one or more BAM/SAM/CAS file(s) * ```blobtools seqfilter``` can filter FASTA files based on a list of sequence names * ```blobtools taxify``` can annotate "taxid" field in Taxonomy files by using a TAXID file