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infoassembly
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Display information about assemblies
Description
infoassembly writes statistics for a sequence assembly.
The initial release is a basic version. More output can be added.
Please contact the authors with suggestions.
Algorithm
None.
Usage
Here is a sample session with infoassembly
% 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
Command line arguments
Display information about assemblies
Version: EMBOSS:6.6.0.0
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
-squick boolean Read id and sequence only
-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
Input file format
The input is a standard EMBOSS assembly query.
The major assembly sources are files in SAM and BAM format.
infoassembly reads a sequnece assembly.
Input files for usage example
File: samspec1.4example.sam
@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 ATAGCTTC
AGC *
r003 16 ref 29 30 6H5M * 0 0 TAGGC
* NM:i:0
r001 83 ref 37 30 9M = 7 -39 CAGCGCCA
T *
Input files for usage example 2
File: xxx.sam
@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
Input files for usage example 3
File: samspec1.4example.ref.fasta
>ref
AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
Output file format
infoassembly writes a simple text report.
Output files for usage example 2
File: qualsdist.txt
#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
Output files for usage example 4
File: gcbias.txt
# 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
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
assemblyget Get assembly of sequence reads
Author(s)
Mahmut Uludag
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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