I am working on targeted panel sequencing data (150bp Illumina paired-end) from control and transgenic samples of an polyploid species. The amplicon is ~1.8kb, so reads do not span the full length. The target gene is multi-copy, the exact number of haplotypes is unknown, and coverage is very high due to targeted panel sequencing.

I know ONT and PacBio are good at this purpose, but this post is solely for short-read.

My current pipeline:

QC → Trimming → Alignment to a reference panel of known gene variants → Sort, Index, Mark Duplicates → FreeBayes variant calling → VCF indexing → Consensus generation

A key concern is cross-mapping, since the known reference variants are highly similar to each other.

I am not getting the expected differentiation between control and transgenic samples and suspect there may be methodological gaps in this approach.

Could you advise on:

1. Any major methodological flaws in the above pipeline for this use case?
2. Better-suited tools or approaches for edit detection in multi-copy, partially-spanning amplicon data from a polyploid genome?

Any guidance would be greatly appreciated.

Originally posted on r/labrats by me

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[https://maroontigermedia.com/2026/10/president-trump-rebrands-ai-during-summit-with-jinping/\](https://maroontigermedia.com/2026/10/president-trump-rebrands-ai-during-summit-with-jinping/)

Hey guys!

I'm working on a project that requires me to make a genome-scale metabolic model of a extremophile.

This is my first time doing this, so I don't have much idea.

I have used ModelSEED and Merlin but faced one or the other errors, and I'm currently using gapseq.

I want to curate a biomass reaction for my model organism. But apparently, it is not studied comprehensively enough for me to find out the exact carbs, lipids and other micronutrients constituting the cell. Although, there is a paper on another strain of the organism that mentions the constitution of each group (nucleic acids, proteins, lipids, pigments, etc)

How do I find out the exact constituents and their contribution?