|   | assemblyget | 
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| % assemblyget bam::samspec1.4example.bam -oformat sam -auto | 
Go to the input files for this example
Go to the output files for this example
| 
Get assembly of sequence reads
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-assembly]          assembly   (no help text) assembly value
  [-outassembly]       outassembly (no help text) outassembly value
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-assembly" associated qualifiers
   -cbegin1            integer    Start of the contig/consensus sequences
   -cend1              integer    End of the contig/consensus sequences
   -iformat1           string     Input assembly format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -idbname1           string     User-provided database name
   "-outassembly" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Assembly output format
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-assembly] (Parameter 1) | assembly | (no help text) assembly value | Assembly of sequence reads | |
| [-outassembly] (Parameter 2) | outassembly | (no help text) outassembly value | Assembly of sequence reads | |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-assembly" associated assembly qualifiers | ||||
| -cbegin1 -cbegin_assembly | integer | Start of the contig/consensus sequences | Any integer value | 0 | 
| -cend1 -cend_assembly | integer | End of the contig/consensus sequences | Any integer value | 0 | 
| -iformat1 -iformat_assembly | string | Input assembly format | Any string | |
| -iquery1 -iquery_assembly | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_assembly | integer | Input start position offset | Any integer value | 0 | 
| -idbname1 -idbname_assembly | string | User-provided database name | Any string | |
| "-outassembly" associated outassembly qualifiers | ||||
| -odirectory2 -odirectory_outassembly | string | Output directory | Any string | |
| -oformat2 -oformat_outassembly | string | Assembly output format | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
The input is a standard EMBOSS assembly query.
The major assembly sources are files in SAM and BAM format.
This file contains non-printing characters and so cannot be displayed here.
The output is a standard EMBOSS assembly query.
The major assembly formats are files in SAM and BAM format.
| @HD VN:1.3 SO:coordinate @PG ID:assemblyget VN:6.6.0.0 CL:[-assembly] bam::../../data/samspec1.4example.bam -oformat sam -auto @SQ SN:ref LN:45 r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTG * r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC * r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * | 
| Program name | Description | 
|---|---|
| infoassembly | Display information about assemblies | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.