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# System prepended metadata

title: A million reasons why your genome assembly sucks in 2021

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# A million reasons why your genome assembly sucks in 2021
[TOC]

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## Sampling, sequencing, and genome characteristics

### You sequenced more than one genome (contamination)

### You sequenced more than one genotype

### You sequenced the wrong genotype

### Your karyotype assumption was wrong, and you didn't even check

### You saved cents on Illumina sequencing
Shorter reads, lower coverage, PCR'ed libraries

### You sequenced too short an insert size


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## Raw data QC and preparation

### You did not check k-mer spectra

### You trimmed the Illumina reads


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## Assembly

### You collapsed very different haplotypes

### Your mosaic strategy is flawed

### You polished away your differences

### You used an obsolete assembler/scaffolder with known limitations

### You just run the latest shiny thingy around

### You overfitted your parameters

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## Assembly QC

### You used BUSCO to check completeness

BUSCO is a ROUGH sanity check.

### You choose on N50

### You did not check k-mer spectra

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## Publication and availability

## You did not make your final assembly available

## You did not make your raw data available

## Your methods are incomplete

## You did not make your intermediate assemblies available
