Percentage of coverage of contigs (genomes) #147
Replies: 4 comments 3 replies
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Hi,
Would covered_fraction suit?
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Ben Woodcroft
Group leader, Centre for Microbiome Research, QUT
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From: Sergey Potapov ***@***.***>
Sent: Tuesday, December 27, 2022 10:40:20 AM
To: wwood/CoverM ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [wwood/CoverM] Percentage of coverage of contigs (genomes) (Discussion #147)
Dear developers! Thanks a lot for the program!
I have one question (or guesses)
I have bam files with genome aligned reads. To know the most covered genome, I need to know the percentage coverage for each genome. I did not find this function in the description. Is it advisable to do so? For example, I have several genomes, and by the percentage of coverage, I can judge the completeness of the coverage and thus identify the best coverage for the genome.
It seemed to me that this is done by the function relative_abundance
But in this way it seems impossible to calculate the percentage of coverage for contigs.
coverm genome --bam-files /home/sergey/CoverM/*.bam -m relative_abundance -t 16 --output-file /home/sergey/CoverM/out.txt
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Thanks for the answer! |
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Yes
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Ben Woodcroft
Group leader, Centre for Microbiome Research, QUT
…________________________________
From: Sergey Potapov ***@***.***>
Sent: Tuesday, December 27, 2022 3:32:22 PM
To: wwood/CoverM ***@***.***>
Cc: Ben J Woodcroft ***@***.***>; Comment ***@***.***>
Subject: Re: [wwood/CoverM] Percentage of coverage of contigs (genomes) (Discussion #147)
Thanks for the answer!
--min-covered-fraction default: 10
10 Is it a percentage?
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Thank you! |
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Just to clarify what Ben was saying. To get the covered fraction for input genomes you would want to use something like the following command: That command will output both the relative abundance, fraction of the genome that is covered by reads, and the trimmed mean coverage. The Rhys |
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Dear, Rhys! |
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Dear developers! Thanks a lot for the program!
I have one question (or guesses)
I have bam files with genome aligned reads. To know the most covered genome, I need to know the percentage coverage for each genome. I did not find this function in the description. Is it advisable to do so? For example, I have several genomes, and by the percentage of coverage, I can judge the completeness of the coverage and thus identify the best coverage for the genome.
It seemed to me that this is done by the function relative_abundance
But in this way it seems impossible to calculate the percentage of coverage for contigs.
coverm genome --bam-files /home/sergey/CoverM/*.bam -m relative_abundance -t 16 --output-file /home/sergey/CoverM/out.txtBeta Was this translation helpful? Give feedback.
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