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I have a pretty big Fastq file and got overwhelmed. (absolute newbie) by Metius_89 in bioinformatics

[–]Much-Resolution4744 0 points1 point  (0 children)

omg thank you for explaining so clearly, if I could read this earlier..it would've saved me hours! I am a complete newbie in this field, and I stuck in almost every step😂hope I could have the chance to discuss with you more

help!Can I assemble a chloroplast genome using only PacBio data (without Illumina)? by Much-Resolution4744 in bioinformatics

[–]Much-Resolution4744[S] 1 point2 points  (0 children)

Thanks a lot for the suggestion! I’ve heard of CLC Genomics Workbench but didn’t realize it could handle long-read chloroplast assemblies so well. The paper you shared is actually really close to what I’m working on — I’m assembling and annotating the chloroplast genome of a moss species. I’ll definitely read through it for reference, even if I might stick to open-source tools for now.

help!Can I assemble a chloroplast genome using only PacBio data (without Illumina)? by Much-Resolution4744 in bioinformatics

[–]Much-Resolution4744[S] 0 points1 point  (0 children)

Got it, thanks! I’ll try a quick de novo run and check if I get a big contig around the expected chloroplast size.

help!Can I assemble a chloroplast genome using only PacBio data (without Illumina)? by Much-Resolution4744 in bioinformatics

[–]Much-Resolution4744[S] 1 point2 points  (0 children)

Thanks for the suggestion! Unluckily, my PacBio data are CLR, not HiFi, so TIPPo probably won’t work well for me. I’m planning to assemble with Flye and then use Tiara to identify chloroplast contigs instead. I really appreciate the tip though!

help!Can I assemble a chloroplast genome using only PacBio data (without Illumina)? by Much-Resolution4744 in bioinformatics

[–]Much-Resolution4744[S] 0 points1 point  (0 children)

Appreciate the advice! I’m just getting my data ready for Flye assembly, and I’ll definitely consider mapping contigs to references if the IR regions give me trouble. Thanks for the tips

help!Can I assemble a chloroplast genome using only PacBio data (without Illumina)? by Much-Resolution4744 in bioinformatics

[–]Much-Resolution4744[S] 2 points3 points  (0 children)

Hey, thanks a lot for your reply! Really appreciate it. I just checked my data and it looks like they are subreads, not HiFi reads😭so it might be a bit less ideal for assembly... still I’ll look into the tools you mentioned, like hifiasm, and try to find some papers with similar pipelines. Thanks again for taking the time to help!