Filter reads using digital normalization via k-mer abundances
normalize-by-median.py
macros.xml
save_countgraph == True
.keep.
By default, Paired end reads will be considered together; if either read will
be kept, then both will be kept. (This keeps both reads from a fragment, and
helps with retention of repeats.) Unpaired reads are treated individually.
If `--paired` is set then proper pairing is required and the tool will exit on
unpaired reads, although `--unpaired-reads` can be used to supply a file of
orphan reads to be read after the paired reads.
`--force_single` will ignore all pairing information and treat reads
individually.
With `-s`/`--savegraph`, the k-mer countgraph will be saved to the specified
file after all sequences have been processed. `--loadgraph` will load the
specified k-mer countgraph before processing the specified files. Note
that the countgraph is in same format as those produced by
`load-into-counting.py` and consumed by `abundance-dist.py`.
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