contributors:team_3:filter
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contributors:team_3:filter [2015/04/15 00:04] jolespin created |
contributors:team_3:filter [2015/07/28 06:03] ceisenhart ↷ Page moved from filter to contributors:2015:team_3:filter |
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| - | $ sga filter --help | + | $ sga filter --help |
| - | Usage: sga filter [OPTION] ... READSFILE | + | Usage: sga filter [OPTION] ... READSFILE |
| - | Remove reads from a data set. | + | Remove reads from a data set. |
| - | The currently available filters are removing exact-match duplicates | + | The currently available filters are removing exact-match duplicates |
| - | and removing reads with low-frequency k-mers. | + | and removing reads with low-frequency k-mers. |
| - | Automatically rebuilds the FM-index without the discarded reads. | + | Automatically rebuilds the FM-index without the discarded reads. |
| - | --help display this help and exit | + | --help display this help and exit |
| - | -v, --verbose display verbose output | + | -v, --verbose display verbose output |
| - | -p, --prefix=PREFIX use PREFIX for the names of the index files (default: prefix of the input file) | + | -p, --prefix=PREFIX use PREFIX for the names of the index files (default: prefix of the input file) |
| - | -o, --outfile=FILE write the qc-passed reads to FILE (default: READSFILE.filter.pass.fa) | + | -o, --outfile=FILE write the qc-passed reads to FILE (default: READSFILE.filter.pass.fa) |
| - | -t, --threads=NUM use NUM threads to compute the overlaps (default: 1) | + | -t, --threads=NUM use NUM threads to compute the overlaps (default: 1) |
| - | -d, --sample-rate=N use occurrence array sample rate of N in the FM-index. Higher values use significantly | + | -d, --sample-rate=N use occurrence array sample rate of N in the FM-index. Higher values use significantly |
| - | less memory at the cost of higher runtime. This value must be a power of 2 (default: 128) | + | less memory at the cost of higher runtime. This value must be a power of 2 (default: 128) |
| - | --no-duplicate-check turn off duplicate removal | + | --no-duplicate-check turn off duplicate removal |
| - | --substring-only when removing duplicates, only remove substring sequences, not full-length matches | + | --substring-only when removing duplicates, only remove substring sequences, not full-length matches |
| - | --no-kmer-check turn off the kmer check | + | --no-kmer-check turn off the kmer check |
| - | --kmer-both-strand mimimum kmer coverage is required for both strand | + | --kmer-both-strand mimimum kmer coverage is required for both strand |
| - | --homopolymer-check check reads for hompolymer run length sequencing errors | + | --homopolymer-check check reads for hompolymer run length sequencing errors |
| - | --low-complexity-check filter out low complexity reads | + | --low-complexity-check filter out low complexity reads |
| - | K-mer filter options: | + | K-mer filter options: |
| - | -k, --kmer-size=N The length of the kmer to use. (default: 27) | + | -k, --kmer-size=N The length of the kmer to use. (default: 27) |
| - | -x, --kmer-threshold=N Require at least N kmer coverage for each kmer in a read. (default: 3) | + | -x, --kmer-threshold=N Require at least N kmer coverage for each kmer in a read. (default: 3) |
| - | Report bugs to js18@sanger.ac.uk | + | Report bugs to js18@sanger.ac.uk |
| </code> | </code> | ||
contributors/team_3/filter.txt · Last modified: 2015/09/02 16:24 by ceisenhart
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