{"__v":11,"_id":"57619476ab49980e008a56b0","category":{"__v":0,"_id":"57619455a7c9f729009a74e0","project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-15T17:45:57.617Z","from_sync":false,"order":5,"slug":"file-descriptions","title":"File formats"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-15T17:46:30.057Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Why is it needed?\"\n}\n[/block]\nA [coverage file](doc:coverage-file)  contains information regarding the base/read coverage of each contig of an [assembly file](doc:assembly-file). Assuming an unbiased sequencing process, the base/read coverage reflects the molarity of the DNA molecule (represented by the sequence in the assembly) that went into the sequencing reaction. \n\nThe coverage information parsed by ```blobtools``` is: \n\n\n* Base coverage \n   * is used in the log-scaled y-axis in a [blobplot](doc:blobplot-1) \n   * is used in both, log-scaled x-axis and y-axis in a [covplot](doc:covplot-1) \n\n\n* Total number of reads and number of mapped reads\n * is used in the first two bars of a [readcovplot](doc:readcovplot) \n\n\n* Read coverage  \n  * is used in subsequent bars of a [readcovplot](doc:readcovplot) \n\n\nThe details on how ```blobtools``` parses coverage information please refer to [coverage parsing](doc:coverage-parsing).\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"File formats\"\n}\n[/block]\n## Mapping files\n* contain all the information needed for ```blobtools create```\n* the following formats are supported:\n * [BAM file](https://samtools.github.io/hts-specs/SAMv1.pdf) (binary SAM)\n * [SAM file](https://samtools.github.io/hts-specs/SAMv1.pdf)\n * [CAS file](http://resources.qiagenbioinformatics.com/manuals/clcassemblycell/current/index.php?manual=Cas_File_Format.html)\n\n\n## Assembly files\n* [Assembly files](doc:assembly-file) generated by certain genome assembly programs contain coverage information in the header lines. \n* ```blobtools create``` is able to parse this information if the assembly type is specified using the ```-y```argument. \n* However, this only includes base-coverage and hence does not allow plotting [readcovplots](doc:readcovplot). \n* The output of the following assemblers is supported:\n * [SPAdes](http://spades.bioinf.spbau.ru/release3.8.1/manual.html)\n * [Velvet](https://www.ebi.ac.uk/~zerbino/velvet/)\n * [Platanus](http://platanus.bio.titech.ac.jp/)\n\n## COV files \n* COV files are a custom file-format written by ```blobtools map2cov``` and  ```blobtools create``` (after parsing a mapping file, a COV file is written automatically for future use) \n * they contain all the information needed for ```blobtools create```.\n * their use is encouraged since parsing a COV file requires less time than parsing a mapping file. \n * an example of a COV file is shown below \n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"## blobtools v0.9.19\\n## Total Reads = 15313\\n## Mapped Reads = 15313\\n## Unmapped Reads = 0\\n## Source(s) : test_files/mapping_1.bam\\n# contig_id\\tread_cov\\tbase_cov\\ncontig_1    369       90.406\\ncontig_2    844       168.409\\ncontig_3    188       43.761\\ncontig_4    2096      456.313\\ncontig_5    456       163.557\\ncontig_6    52        25.88\\ncontig_7    1005      52.312\\ncontig_8    1008      91.742\\ncontig_9    554       74.757\\ncontig_10   8741      310.634\\n\",\n      \"language\": \"text\",\n      \"name\": \"test_files/mapping_1.bam.cov\"\n    }\n  ]\n}\n[/block]","excerpt":"","slug":"coverage-file","type":"basic","title":"coverage file"}
[block:api-header] { "type": "basic", "title": "Why is it needed?" } [/block] A [coverage file](doc:coverage-file) contains information regarding the base/read coverage of each contig of an [assembly file](doc:assembly-file). Assuming an unbiased sequencing process, the base/read coverage reflects the molarity of the DNA molecule (represented by the sequence in the assembly) that went into the sequencing reaction. The coverage information parsed by ```blobtools``` is: * Base coverage * is used in the log-scaled y-axis in a [blobplot](doc:blobplot-1) * is used in both, log-scaled x-axis and y-axis in a [covplot](doc:covplot-1) * Total number of reads and number of mapped reads * is used in the first two bars of a [readcovplot](doc:readcovplot) * Read coverage * is used in subsequent bars of a [readcovplot](doc:readcovplot) The details on how ```blobtools``` parses coverage information please refer to [coverage parsing](doc:coverage-parsing). [block:api-header] { "type": "basic", "title": "File formats" } [/block] ## Mapping files * contain all the information needed for ```blobtools create``` * the following formats are supported: * [BAM file](https://samtools.github.io/hts-specs/SAMv1.pdf) (binary SAM) * [SAM file](https://samtools.github.io/hts-specs/SAMv1.pdf) * [CAS file](http://resources.qiagenbioinformatics.com/manuals/clcassemblycell/current/index.php?manual=Cas_File_Format.html) ## Assembly files * [Assembly files](doc:assembly-file) generated by certain genome assembly programs contain coverage information in the header lines. * ```blobtools create``` is able to parse this information if the assembly type is specified using the ```-y```argument. * However, this only includes base-coverage and hence does not allow plotting [readcovplots](doc:readcovplot). * The output of the following assemblers is supported: * [SPAdes](http://spades.bioinf.spbau.ru/release3.8.1/manual.html) * [Velvet](https://www.ebi.ac.uk/~zerbino/velvet/) * [Platanus](http://platanus.bio.titech.ac.jp/) ## COV files * COV files are a custom file-format written by ```blobtools map2cov``` and ```blobtools create``` (after parsing a mapping file, a COV file is written automatically for future use) * they contain all the information needed for ```blobtools create```. * their use is encouraged since parsing a COV file requires less time than parsing a mapping file. * an example of a COV file is shown below [block:code] { "codes": [ { "code": "## blobtools v0.9.19\n## Total Reads = 15313\n## Mapped Reads = 15313\n## Unmapped Reads = 0\n## Source(s) : test_files/mapping_1.bam\n# contig_id\tread_cov\tbase_cov\ncontig_1 369 90.406\ncontig_2 844 168.409\ncontig_3 188 43.761\ncontig_4 2096 456.313\ncontig_5 456 163.557\ncontig_6 52 25.88\ncontig_7 1005 52.312\ncontig_8 1008 91.742\ncontig_9 554 74.757\ncontig_10 8741 310.634\n", "language": "text", "name": "test_files/mapping_1.bam.cov" } ] } [/block]