contributors:team_3:preprocess
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contributors:team_3:preprocess [2015/04/15 00:04] jolespin |
contributors:team_3:preprocess [2015/04/15 00:07] jolespin |
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| <code> | <code> | ||
| - | $ sga preprocess --help | + | $ sga preprocess --help |
| - | Usage: sga preprocess [OPTION] READS1 READS2 ... | + | Usage: sga preprocess [OPTION] READS1 READS2 ... |
| - | Prepare READS1, READS2, ... data files for assembly | + | Prepare READS1, READS2, ... data files for assembly |
| - | If pe-mode is turned on (pe-mode=1) then if a read is discarded its pair will be discarded as well. | + | If pe-mode is turned on (pe-mode=1) then if a read is discarded its pair will be discarded as well. |
| - | --help display this help and exit | + | --help display this help and exit |
| - | -v, --verbose display verbose output | + | -v, --verbose display verbose output |
| - | --seed set random seed | + | --seed set random seed |
| - | Input/Output options: | + | Input/Output options: |
| - | -o, --out=FILE write the reads to FILE (default: stdout) | + | -o, --out=FILE write the reads to FILE (default: stdout) |
| - | -p, --pe-mode=INT 0 - do not treat reads as paired (default) | + | -p, --pe-mode=INT 0 - do not treat reads as paired (default) |
| - | 1 - reads are paired with the first read in READS1 and the second | + | 1 - reads are paired with the first read in READS1 and the second |
| - | read in READS2. The paired reads will be interleaved in the output file | + | read in READS2. The paired reads will be interleaved in the output file |
| - | 2 - reads are paired and the records are interleaved within a single file. | + | 2 - reads are paired and the records are interleaved within a single file. |
| - | --pe-orphans=FILE if one half of a read pair fails filtering, write the passed half to FILE | + | --pe-orphans=FILE if one half of a read pair fails filtering, write the passed half to FILE |
| - | Conversions/Filtering: | + | Conversions/Filtering: |
| - | --phred64 convert quality values from phred-64 to phred-33. | + | --phred64 convert quality values from phred-64 to phred-33. |
| - | --discard-quality do not output quality scores | + | --discard-quality do not output quality scores |
| - | -q, --quality-trim=INT perform Heng Li's BWA quality trim algorithm. | + | -q, --quality-trim=INT perform Heng Li's BWA quality trim algorithm. |
| - | Reads are trimmed according to the formula: | + | Reads are trimmed according to the formula: |
| - | argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT | + | argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT |
| - | where l is the original read length. | + | where l is the original read length. |
| - | -f, --quality-filter=INT discard the read if it contains more than INT low-quality bases. | + | -f, --quality-filter=INT discard the read if it contains more than INT low-quality bases. |
| - | Bases with phred score <= 3 are considered low quality. Default: no filtering. | + | Bases with phred score <= 3 are considered low quality. Default: no filtering. |
| - | The filtering is applied after trimming so bases removed are not counted. | + | The filtering is applied after trimming so bases removed are not counted. |
| - | Do not use this option if you are planning to use the BCR algorithm for indexing. | + | Do not use this option if you are planning to use the BCR algorithm for indexing. |
| - | -m, --min-length=INT discard sequences that are shorter than INT | + | -m, --min-length=INT discard sequences that are shorter than INT |
| - | this is most useful when used in conjunction with --quality-trim. Default: 40 | + | this is most useful when used in conjunction with --quality-trim. Default: 40 |
| - | -h, --hard-clip=INT clip all reads to be length INT. In most cases it is better to use | + | -h, --hard-clip=INT clip all reads to be length INT. In most cases it is better to use |
| - | the soft clip (quality-trim) option. | + | the soft clip (quality-trim) option. |
| - | --permute-ambiguous Randomly change ambiguous base calls to one of possible bases. | + | --permute-ambiguous Randomly change ambiguous base calls to one of possible bases. |
| - | If this option is not specified, the entire read will be discarded. | + | If this option is not specified, the entire read will be discarded. |
| - | -s, --sample=FLOAT Randomly sample reads or pairs with acceptance probability FLOAT. | + | -s, --sample=FLOAT Randomly sample reads or pairs with acceptance probability FLOAT. |
| - | --dust Perform dust-style filtering of low complexity reads. | + | --dust Perform dust-style filtering of low complexity reads. |
| - | --dust-threshold=FLOAT filter out reads that have a dust score higher than FLOAT (default: 4.0). | + | --dust-threshold=FLOAT filter out reads that have a dust score higher than FLOAT (default: 4.0). |
| - | --suffix=SUFFIX append SUFFIX to each read ID | + | --suffix=SUFFIX append SUFFIX to each read ID |
| - | Adapter/Primer checks: | + | Adapter/Primer checks: |
| - | --no-primer-check disable the default check for primer sequences | + | --no-primer-check disable the default check for primer sequences |
| - | -r, --remove-adapter-fwd=STRING | + | -r, --remove-adapter-fwd=STRING |
| - | -c, --remove-adapter-rev=STRING Remove the adapter STRING from input reads. | + | -c, --remove-adapter-rev=STRING Remove the adapter STRING from input reads. |
| - | Report bugs to js18@sanger.ac.uk | + | Report bugs to js18@sanger.ac.uk |
| </code> | </code> | ||
contributors/team_3/preprocess.txt · Last modified: 2015/07/28 06:00 by ceisenhart
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