Where:
Run SOAPdenovo2 in the same folder as your DNA-seq reads. (Use File
--> OpenDir to open a new window in your reads folder.)
Input:
Input files selected in the blreads table are ignored! Specify
your read files in Libraries:
Libraries - SOAPdenovo2 asks the user to specify
one or more libraries of read files and parameters to use with
those read files. For example, reads with 300 nt inserts would be
in one library, and reads with a 400 nt inserts must be in a
different library.
The Parameters tab allows you to specify up to 4 pairs of reads
for the first library. The additionalLIBS tab lets you specify up
to three libraries, each with four sets of read files. For each
library, all reads in the library will be processed with the
following parameters:
- Use reads for
contigs and scaffolds, contigs only or scaffolds only
- Average insert size
- reversal of reads in
the library (Yes or No)
- rank - use in first
round (1) or scaffolding, or in second round (2)
- maximum read length
Paired-end vs. single end
reads - For single end reads, choose a Left pair read file and
leave the Right filename blank.
For each library, don't forget to click "Yes" on the first line to
add that library to the input.
Output:
The default "../reads.trimmed.corrected.SOAPdenovo2" means that output files
will be written to a folder in the parent folder (..) called
SOAPdenovo2.
The most useful human-readable output files:
soapdenovo2.log - Detailed progress on the assembly.
<prefix>.scaffStatistics - Statistics on
contigs and scaffolds, including numbers such as N50, base composition etc.