<p>I am new to pacbio sequencing data. I just did some alignment of pacbio HiFI data using pbmm2. I have the bam now, I would like to collect some metrics on the alignment. I used to work on the illumina data, I used picard CollectAlignmentSummaryMetrics, CollectGcBiasMetrics, CollectInsertSizeMetrics to collect a series of alignment metrics.
I was wondering if there is similar tools for pacbio data. I searched and did not find an answer.</p>
<p>We are mainly interested in aligned rate, sequence length, coverage, accuracy, and GC content. So I write some scripts for it. These scripts are inside the nextflow, the input is the bam file</p>
<pre><code>samtools flagstat <span class="math-container">$bam \
 | head -8 \
 | tr " " ","  \
 | tr "+" " " \
 | awk -F',' '{ print $1, $3}' \
 | paste - - - - - - - -  \
 | awk '{print $1, $3, $5, $7, $9, $11, $2, $4, $6, $8, $10, $</span>12 }' &gt;  align_prp
 
 samtools depth <span class="math-container">$bam \
 |  awk '{sum+=$3; sumsq+=$3*$</span>3} END { print sum/NR, sqrt(sumsq/NR - (sum/NR)**2)}' &gt; coverage
 
 samtools view <span class="math-container">$bam \
 | awk '{ $35=length($10); sum+=$35; sumsq+=$35*$</span>35} END { print sum/NR, sqrt(sumsq/NR - (sum/NR)**2)}' &gt; length
 

 
 samtools view  <span class="math-container">$bam \
 | cut -f 10 \
 | fold -w 1 \
 | awk '($</span>1==&quot;G&quot; || $1==&quot;C&quot;) {N++;} END {print (N/(1.0*NR)*100);}' &gt; GC_content
</code></pre>
<p>But I am still interested to know if there are some package available there.</p>

CC BY-SA 4.0
2023-06-09T20:38:27.150Z
Is this useful at all? https://www.biostars.org/p/9494195/
Ram RS
CC BY-SA 4.0
2023-06-09T20:43:01.603Z
No, I am not accessible to Revio, Sequel II and IIe systems.
cautree
CC BY-SA 4.0
2024-06-12T20:40:42.210Z
Have you tried --log-level INFO in pbmm2 align
María José
<phylogenetics><pacbio>
Pacbio HIFI pbmm2 alignment metrics
# Pacbio HIFI pbmm2 alignment metrics

(Asked by: username_0 on 2023-06-09)

I am new to pacbio sequencing data. I just did some alignment of pacbio HiFI data using pbmm2. I have the bam now, I would like to collect some metrics on the alignment. I used to work on the illumina data, I used picard CollectAlignmentSummaryMetrics, CollectGcBiasMetrics, CollectInsertSizeMetrics to collect a series of alignment metrics.
I was wondering if there is similar tools for pacbio data. I searched and did not find an answer.
We are mainly interested in aligned rate, sequence length, coverage, accuracy, and GC content. So I write some scripts for it. These scripts are inside the nextflow, the input is the bam file
samtools flagstat $bam \
 | head -8 \
 | tr " " ","  \
 | tr "+" " " \
 | awk -F',' '{ print $1, $3}' \
 | paste - - - - - - - -  \
 | awk '{print $1, $3, $5, $7, $9, $11, $2, $4, $6, $8, $10, $12 }' >  align_prp
 
 samtools depth $bam \
 |  awk '{sum+=$3; sumsq+=$3*$3} END { print sum/NR, sqrt(sumsq/NR - (sum/NR)**2)}' > coverage
 
 samtools view $bam \
 | awk '{ $35=length($10); sum+=$35; sumsq+=$35*$35} END { print sum/NR, sqrt(sumsq/NR - (sum/NR)**2)}' > length
 

 
 samtools view  $bam \
 | cut -f 10 \
 | fold -w 1 \
 | awk '($1=="G" || $1=="C") {N++;} END {print (N/(1.0*NR)*100);}' > GC_content

But I am still interested to know if there are some package available there.

**Tags:** phylogenetics, pacbio
> **Comments:**
> **username_1**: Is this useful at all? https://www.biostars.org/p/9494195/  
> **username_0**: No, I am not accessible to Revio, Sequel II and IIe systems.  
> **username_2**: Have you tried --log-level INFO in pbmm2 align  

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## 0 answers

