Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.
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AllpathsLG 44837
Community rating: ?????
AllpathsLG App that runs on Lonestar.
Quick Start
- To
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- use AllpathsLG 44837, import your
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Test Data
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- sequencing reads in fastq format. Enter paired reads in the paired read sections. All libraries must have a name. All paired libraries must have an entry for pair distance and the estimated error in this value. The type of library should be entered - fragment or jumping. Usually this setting will determine the orientation of the reads, but the Reads 4 section requires a setting for orientation and allows the unlikely situation that fragment reads are not forward-reverse or jumping reads are not reverse-forward. Set the time according to expected run. Maximum memory available with be 1 TB. Maximum run time 48 hours, so large genomes will not likely assemble in that time. If indications are that that is a limiting factor, you can try Random downsample reads to reduce the load. Be sure to enter a value for sequence format for each library (fragment, jumping respectively).
- Resources: http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-#ALLPATHS
Test Data
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Input File(s)
Use
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the "frag" reads (180 bp spacing, +- 30) as a fragment library labeled "fragment" (or anything really) from the directory above as test input.
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Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.
- Default parameters only, no further configuration needed.
OR
- Use these parameters within the DE app interface:
- parameter name - value/setting
- parameter name - value/setting
Use the "shortjump" reads (3500 bp spacing, +- 500) as a jumping library labeled "jumpie". Run for 4 hours. Check "Override Phred" to make sure the assembly isn't stopped because of questions about the Phred setting.
Output File(s)
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Outputs will include a genome.scf.fasta file for the scaffolds, and a genome.ctg.fasta for contigs.
Tool Source for App
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