Difference between revisions of "Filter SPAdes output"
From BioUML platform
(Created page with "==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 ...") |
|||
| Line 3: | Line 3: | ||
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. | 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 | + | 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. |
Latest revision as of 14:24, 27 March 2019
[edit] 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.
