Answers.Body: <p>To expand on the comment by Devon Ryan, what you really need are (A.) bam alignment files for each individual and (B.) VCF files for each individual showing all of their genomic variants (with respect to the reference human genome).  You mentioned that you had fastq files and that you converted them into fasta files.  Do you know if the bam files and VCF files are also available for download anywhere?</p>
  
  <p>If the bam files are not available you will have generate them using sequence aligner software (for example: bwa-mem).  With the bam files you can calculate the average depth of coverage (and many other things).</p>
  
  <p>If the VCF files are not available then you will have to generate them from the bam files using variant calling software (for example, the GATK package from the Broad Institute).</p>
  
  <p>In terms of assessing the quality of the sequence runs, a commonly applied tool is name FastQC, but once again, it uses fastq formatted files as input, not fasta files.</p>
  
  <p>The main use for fasta formatted files these days seems to be for compact storage of various reference genomes from different genome sequencing projects (using gzip or similar type of compression).</p>
  
  <p>With the VCF files for each individual in hand you should be able to begin addressing your other questions regarding the frequency of shared variants, etc.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-05T22:13:30.223Z
Answers.Text: .bam and VCF aren't available. Is there any statistics that a valid genome should follow. Like frequencies of bases or ngram bases? Can you recommend of tools to generate VCF and .bam files from .fasta?
Answers.UserDisplayName: 0x90
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Answers.CreationDate: 2018-08-05T17:49:29.547Z
Answers.LastActivityDate: 2018-08-05T17:49:29.547Z
Answers.UserDisplayName: mdperry
Body: <p>I have assembled 3 <code>.fasta</code> files from contigs in<code>fastq</code> format of 3 different Homo sapiens.  </p>
  
  <p>I would like to see if the assembled genomes which are in <code>.fasta</code> format are in good quality or not. In addition, I would be happy to see heritages of genes from the maternal or the parental genomes. </p>
  
  <p>More specifically, I have 3 <code>.fasta</code> files of a mother, father and daughter. </p>
  
  <ol>
  <li>How can I see they are indeed the biological parents?</li>
  <li>How can I study what genes were inherited from whom of the parents? </li>
  <li>How can I assess the quality of the assembled genomes? Is there a standard way to do that? </li>
  <li>Is there a simple frequency analysis of bases n-grams I can use?</li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-31T06:58:02.713Z
Comments.Text: Are these for humans? I imagine it'd be easier to work with VCF files than assembled fasta files.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-31T10:34:16.030Z
Comments.Text: @DevonRyan they are humans
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-01T10:04:50.413Z
Comments.Text: What gene is this? Or it is the whole genome in a single fasta file? If the later case, if you explain the pipeline you use it might be easier to get an answer via VCF or tandem repeats.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-01T10:40:05.983Z
Comments.Text: @Llopis whole genome
Comments.UserDisplayName: 0x90
Tags: <genome><python><assembly><phylogenetics><phylogeny>
Title: How to assess the quality of assembled .fasta genome files?
ThreadText: # How to assess the quality of assembled .fasta genome files?
  
  (Asked by: username_0 on 2018-07-31)
  
  I have assembled 3 `.fasta` files from contigs in`fastq` format of 3 different Homo sapiens.
  
  I would like to see if the assembled genomes which are in `.fasta` format are in good quality or not. In addition, I would be happy to see heritages of genes from the maternal or the parental genomes.
  
  More specifically, I have 3 `.fasta` files of a mother, father and daughter.
  
  1. How can I see they are indeed the biological parents?
  2. How can I study what genes were inherited from whom of the parents?
  3. How can I assess the quality of the assembled genomes? Is there a standard way to do that?
  4. Is there a simple frequency analysis of bases n-grams I can use?
  
  **Tags:** genome, python, assembly, phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: Are these for humans? I imagine it'd be easier to work with VCF files than assembled fasta files.  
  > **username_0**: @username_1 they are humans  
  > **username_2**: What gene is this? Or it is the whole genome in a single fasta file? If the later case, if you explain the pipeline you use it might be easier to get an answer via VCF or tandem repeats.  
  > **username_0**: @Llopis whole genome  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-08-05. Score: 2
  
  To expand on the comment by username_1 username_1, what you really need are (A.) bam alignment files for each individual and (B.) VCF files for each individual showing all of their genomic variants (with respect to the reference human genome). You mentioned that you had fastq files and that you converted them into fasta files. Do you know if the bam files and VCF files are also available for download anywhere?
  
  If the bam files are not available you will have generate them using sequence aligner software (for example: bwa-mem). With the bam files you can calculate the average depth of coverage (and many other things).
  
  If the VCF files are not available then you will have to generate them from the bam files using variant calling software (for example, the GATK package from the Broad Institute).
  
  In terms of assessing the quality of the sequence runs, a commonly applied tool is name FastQC, but once again, it uses fastq formatted files as input, not fasta files.
  
  The main use for fasta formatted files these days seems to be for compact storage of various reference genomes from different genome sequencing projects (using gzip or similar type of compression).
  
  With the VCF files for each individual in hand you should be able to begin addressing your other questions regarding the frequency of shared variants, etc.
  
  > **Comments:**
  > **username_0**: .bam and VCF aren't available. Is there any statistics that a valid genome should follow. Like frequencies of bases or ngram bases? Can you recommend of tools to generate VCF and .bam files from .fasta?  
  
  ---
  
  