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--- lecture_notes:04-16-2010 [2010/04/16 22:49]
svasili created
+++ lecture_notes:04-16-2010 [2010/04/16 23:27]
svasili
@@ Line 10: / Line 10: @@
   * Kevin ran the assembly tool on POG 454 data under /campusdata/BME235/assemblies/Pog.
   * The README file in the directory contains important information about the assembly.
+  * Info about tools installed is listed in bioinformatic_tools [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]]. Info about how to run the De novo as well as Mapping assembly tools is also included there.
+  * Currently tools are installed under /campusdata/BME235/bin/old_Newbler/.
+  * Its better to run the tool in the current working directory.
+  * Tools with prefix "gs" are not supposed to be run directly.
+  * 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.
+  * 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]].
+    <code>
+newAssembly .
+addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff
+addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff
+runProject -e 50 .
+</code>
+  * -e 50 is an important parameter -> implies expected coverage and it defaults to 50.

Banana Slug Genomics