                                infoassembly



Wiki

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   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
