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infoassembly |
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The initial release is a basic version. More output can be added. Please contact the authors with suggestions.
% infoassembly sam::samspec1.4example.sam stdout -auto Read distribution: ------------------ READ_CATEGORY #READS Av_Read_Length all reads 6 10.33 first of pair 1 9.00 second of pair 1 17.00 pair 2 13.00 unpaired 4 9.00 Contig stats: ------------- CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC ref 45 0.00 6 0 0.00 0.00 |
Go to the input files for this example
Example 2
% infoassembly sam::xxx.sam stdout -auto -qual qualsdist.txt Phred encoding: Sanger / Illumina 1.9 Read distribution: ------------------ READ_CATEGORY #READS Av_Read_Length all reads 2 35.00 first of pair 1 35.00 second of pair 1 35.00 pair 2 35.00 unpaired 0 Contig stats: ------------- CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC chr20 62435964 25.36 2 2 1.97 0.00 |
Go to the input files for this example
Go to the output files for this example
Example 3
% infoassembly sam::../data/samspec1.4example.ref.fasta Read distribution: ------------------ READ_CATEGORY #READS Av_Read_Length all reads 6 10.33 first of pair 1 9.00 second of pair 1 17.00 pair 2 13.00 unpaired 4 9.00 Contig stats: ------------- CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC ref 45 0.00 6 3 1.82 46.67 |
Go to the input files for this example
Example 4
% infoassembly sam::../data/samspec1.4example.ref.fasta -gc gcbias.txt Read distribution: ------------------ READ_CATEGORY #READS Av_Read_Length all reads 6 10.33 first of pair 1 9.00 second of pair 1 17.00 pair 2 13.00 unpaired 4 9.00 Contig stats: ------------- CONTIG LENGTH Mean_QUAL #READS Max DEPTH Mean_DEPTH %GC ref 45 0.00 6 3 1.82 46.67 |
Go to the output files for this example
Display information about assemblies
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-assembly] assembly (no help text) assembly value
[-outassembly] outassembly (no help text) outassembly value
[-gcbiasmetricsoutfile] outfile [*.infoassembly] GC bias metrics
[-qualvaluesdistoutfile] outfile [*.infoassembly] Distribution of quality
values for the reads
Additional (Optional) qualifiers:
-refsequence seqset Reference sequences in the assembly
-windowsize integer [100] The size of windows on the genome that
are used to bin reads. (Any integer value)
-bisulfite boolean [N] If this is true, it is assumed that the
reads were bisulfite treated
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
"-refsequence" associated qualifiers
-sbegin integer Start of each sequence to be used
-send integer End of each sequence to be used
-sreverse boolean Reverse (if DNA)
-sask boolean Ask for begin/end/reverse
-snucleotide boolean Sequence is nucleotide
-sprotein boolean Sequence is protein
-slower boolean Make lower case
-supper boolean Make upper case
-scircular boolean Sequence is circular
-sformat string Input sequence format
-iquery string Input query fields or ID list
-ioffset integer Input start position offset
-sdbname string Database name
-sid string Entryname
-ufo string UFO features
-fformat string Features format
-fopenfile string Features file name
"-outassembly" associated qualifiers
-odirectory2 string Output directory
-oformat2 string Assembly output format
"-gcbiasmetricsoutfile" associated qualifiers
-odirectory3 string Output directory
"-qualvaluesdistoutfile" associated qualifiers
-odirectory4 string Output directory
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 | |
| [-gcbiasmetricsoutfile] (Parameter 3) |
outfile | GC bias metrics | Output file | <*>.infoassembly |
| [-qualvaluesdistoutfile] (Parameter 4) |
outfile | Distribution of quality values for the reads | Output file | <*>.infoassembly |
| Additional (Optional) qualifiers | ||||
| -refsequence | seqset | Reference sequences in the assembly | Readable set of sequences | Required |
| -windowsize | integer | The size of windows on the genome that are used to bin reads. | Any integer value | 100 |
| -bisulfite | boolean | If this is true, it is assumed that the reads were bisulfite treated | Boolean value Yes/No | No |
| 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 | |
| "-refsequence" associated seqset qualifiers | ||||
| -sbegin | integer | Start of each sequence to be used | Any integer value | 0 |
| -send | integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse | boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide | boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein | boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower | boolean | Make lower case | Boolean value Yes/No | N |
| -supper | boolean | Make upper case | Boolean value Yes/No | N |
| -scircular | boolean | Sequence is circular | Boolean value Yes/No | N |
| -sformat | string | Input sequence format | Any string | |
| -iquery | string | Input query fields or ID list | Any string | |
| -ioffset | integer | Input start position offset | Any integer value | 0 |
| -sdbname | string | Database name | Any string | |
| -sid | string | Entryname | Any string | |
| -ufo | string | UFO features | Any string | |
| -fformat | string | Features format | Any string | |
| -fopenfile | string | Features file name | Any string | |
| "-outassembly" associated outassembly qualifiers | ||||
| -odirectory2 -odirectory_outassembly |
string | Output directory | Any string | |
| -oformat2 -oformat_outassembly |
string | Assembly output format | Any string | |
| "-gcbiasmetricsoutfile" associated outfile qualifiers | ||||
| -odirectory3 -odirectory_gcbiasmetricsoutfile |
string | Output directory | Any string | |
| "-qualvaluesdistoutfile" associated outfile qualifiers | ||||
| -odirectory4 -odirectory_qualvaluesdistoutfile |
string | Output directory | 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. infoassembly reads a sequnece assembly.
@CO example from SAM format specification v1.4 @HD VN:1.3 SO:coordinate @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 * |
@HD VN:1.0 @SQ SN:chr20 LN:62435964 @RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 @RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr20 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 |
>ref AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT |
#QUALITY: Phred quality score #BASES: Number of bases with the quality score QUALITY #BASES 5 1 11 2 14 1 17 2 21 1 22 2 24 1 25 2 26 5 27 53 |
# GC bias metrics as described in GcBiasDetailMetrics class # in picard project (picard.sf.net). # The mean base quality are determined via the error rate # of all bases of all reads that are assigned to windows of a GC. GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE 20 5 1 8 1.13333 30 5 2 10 2.26667 40 4 0 0 0 50 11 1 0 0.515152 60 4 1 0 1.41667 70 5 0 0 0 |
| Program name | Description |
|---|---|
| assemblyget | Get assembly of sequence reads |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.