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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Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). Wtdbg2 has two key components: an assembler wtdbg2 and a consenser wtpoa-cns. Executable wtdbg2 assembles raw reads and generates the contig layout and edge sequences in a file "prefix.ctg.lay.gz". Executable wtpoa-cns takes this file as input and produces the final consensus in FASTA.

Quick Start

Test Data

  • Test data for wtpoa-cns can be found directly from Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> wtdbg2 -> wtdbg2_output 

Input File(s)

Use wtdbg_SRR8506728_output.ctg.lay.gz as the input file. 

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.

  • Set output file name to wtpoa_SRR8506728_output.fa
  • All other parameters should be left as default

Output File(s)

This analysis will generate a single FASTA formatted output file of consensus contigs (named as indicated above):

wtpoa_SRR8506728_output.fa

 

Tool Source for App

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