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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
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| 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.