Genome Size Estimation

[NicMAlexandre]

Hello,

This software is very cool. I'm trying to estimate genome size on PacBio reads using your software. The readme mentions that the output stat file can be used as input in GCE and correct_error_reads. What is your general pipeline for using this output to estimate genome size?

Nicolas

[fanagislab]

Hi, Nicolas You can find instructions on these pages: https://github.com/fanagislab/GCE https://github.com/fanagislab/kmerfreq There are two steps: (1) use kmerfreq to count kmer frequency; (2) estimate genome size with kmer frequency. Best regards fanwei@caas.cn From: nicolasalexandre21 Date: 2020-04-21 02:13 To: fanagislab/kmerfreq CC: Subscribed Subject: [fanagislab/kmerfreq] Genome Size Estimation (#2) Hello, This software is very cool. I'm trying to estimate genome size on PacBio reads using your software. The readme mentions that the output stat file can be used as input in GCE and correct_error_reads. What is your general pipeline for using this output to estimate genome size? Nicolas — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[NicMAlexandre]

Thank you! This is very helpful! Nicolas

…

On Mon, Apr 20, 2020 at 6:06 PM fanwei ***@***.***> wrote: Hi, Nicolas You can find instructions on these pages: https://github.com/fanagislab/GCE https://github.com/fanagislab/kmerfreq There are two steps: (1) use kmerfreq to count kmer frequency; (2) estimate genome size with kmer frequency. Best regards ***@***.*** From: nicolasalexandre21 Date: 2020-04-21 02:13 To: fanagislab/kmerfreq CC: Subscribed Subject: [fanagislab/kmerfreq] Genome Size Estimation (#2) Hello, This software is very cool. I'm trying to estimate genome size on PacBio reads using your software. The readme mentions that the output stat file can be used as input in GCE and correct_error_reads. What is your general pipeline for using this output to estimate genome size? Nicolas — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFB633YQSN4SARCD4SUZYIDRNTWP5ANCNFSM4MMVAISA> .

-- Best, Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley nalexandre@berkeley.edu <kiv@berkeley.edu>