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Filter SPAdes output (version 0.1)

Sequences:

Contigs or scaffolds. Make sure you input the corresponding stat file

Contig stats:

Length cut-off:

Contigs with length under that value are shown in red

Coverage cut-off:

Contigs with length under that value are shown in red

Save filtered-out sequences?:

What it does

Using the output of SPAdes (a fasta and a stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under a given length or under a given coverage.

Typically, this is used to discard short contigs, or contaminations. To display a coverage vs. length plot, use the "SPAdes stats" tool in the same package.