AllpathsLG 44837
AllpathsLG 44837
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AllpathsLG App that runs on Lonestar.
Quick Start
To use AllpathsLG 44837, import your 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).
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> allpaths -> rhodo.
Input File(s)
Use the "frag" reads (180 bp spacing, +- 30) as a fragment library labeled "fragment" (or anything really) from the directory above as test input. 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)
Outputs will include a genome.scf.fasta file for the scaffolds, and a genome.ctg.fasta for contigs.
When you are running your own data, make sure that your input files end with a .fastq extension and that the read pairs end with their number. For example, frag_1.fastq and frag_2.fastq