Where:
Run spades in the same folder as your DNA-seq reads. (Use File
--> OpenDir to open a new window in your reads folder.)
Input:
RNAseq reads: Before opening this
menu, select DNA readfiles. For paired-end reads spades,
works with pairs of files. Files can be selected in pairs using
File --> guesspairs.py.
Parameters:
k-mers: Spades repeats the assembly with k-mers over a
range of sizes and chooses the best assembly as the final one. The
k-mers are specified as a comma-separated list eg. 21,33,55.
k-mers must be odd numbers. If k-mers is set to automatic
(default), spades will choose a list of k-mer sizes to try.
The larger the k-mer size, the larger the memory needed. A k-mer
size of 33 should be possible on most desktop machines. Larger
k-mer sizes may require substantially larger memory. As well, for
each k-mer tested, disk space comparable to the size of the input
read files will be needed.
Spades will work its way through the k-mers from smallest to
largest. If spades runs out of memory with larger k-mers, the
results from earlier runs with smaller k-mer sizes can still be
found in the output directory. For example, results from k=33 are
found in the K33 subdirectory.
Output:
The default "../reads.trimmed.corrected.spades" means that output files will
be written to a folder in the parent folder (..) called spades.
The most useful human-readable output files:
spades.log - Detailed progress on the assembly.