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