lecture_notes:04-16-2010
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lecture_notes:04-16-2010 [2010/04/16 23:27] svasili |
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| * Newbler assembly tools take .sff (color space and quality data) files as input and converts them into .fna (fasta file with nucleotide information) files. | * Newbler assembly tools take .sff (color space and quality data) files as input and converts them into .fna (fasta file with nucleotide information) files. | ||
| * Good only with 454 data, is not good on reads < 50bp. | * Good only with 454 data, is not good on reads < 50bp. | ||
| - | * Example to run the tools on data is shown below. The code is taken from [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]]. | + | * Example to run the De novo tool on data is shown below. The code is taken from [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]]. |
| <code> | <code> | ||
| newAssembly . | newAssembly . | ||
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| runProject -e 50 . | runProject -e 50 . | ||
| </code> | </code> | ||
| - | * -e 50 is an important parameter -> implies expected coverage and it defaults to 50. | + | * Where, -e 50 is an important parameter -> implies expected coverage and it defaults to 50. |
lecture_notes/04-16-2010.txt ยท Last modified: 2010/04/20 03:09 by karplus
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