The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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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).
  • Resources: http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-#ALLPATHS

Test Data

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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.


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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

Tool Source for App

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