User Tools

Site Tools


contributors:team_3:preprocess

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
contributors:team_3:preprocess [2015/04/15 00:00]
jolespin created
contributors:team_3:preprocess [2015/07/28 06:00] (current)
ceisenhart ↷ Page moved from preprocess to contributors:team_3:preprocess
Line 1: Line 1:
-    ​$ sga preprocess --help +<​code>​ 
-    Usage: sga preprocess [OPTION] READS1 READS2 ... +$ sga preprocess --help 
-    Prepare READS1, READS2, ... data files for assembly +Usage: sga preprocess [OPTION] READS1 READS2 ... 
-    If pe-mode is turned on (pe-mode=1) then if a read is discarded its pair will be discarded as well.+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.
  
-            ​--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>​
contributors/team_3/preprocess.1429056037.txt.gz · Last modified: 2015/04/15 00:00 by jolespin