EMBOSS: infoassembly

| 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:6.5.6.0

       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

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

## 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	ATAGCTTCAGC	*
    r003	16	ref	29	30	6H5M	*	0	0	TAGGC	*	NM:i:0
    r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT	*

### 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 © 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