---
# System prepended metadata

title: Pilot HybSeq

---

# Pilot HybSeq

### Trim With Fastp
default parameters

### Assemble with HybPiper
default parameters

run stats script 

run heatmap script

run retrieve sequences

```bash=
hybpiper retrieve_sequences dna -t_dna cycad333_targets.fasta --sample_names namelist.txt --fasta_dir FNA
```

### Align with MAFFT

```bash=
parallel -j 20 --eta "mafft --preservecase --auto FNA/{}.FNA > mafft/{}.mafft.fasta" :::: genelist.txt
```

### Trim with TrimAl

```bash=
parallel -j 20 trimal -in mafft/{}.mafft.fasta -out trimal/{}.trimal.fasta -gt 0.5 :::: genelist.txt
```

### Gene trees with iqtree
```bash=
parallel -j 5 --eta iqtree -s {}.trimal.fasta -T 4 -B 1000 -m MFP :::: ../genelist.txt
```

### Species tree with astral
```bash=
cat trimal/*.treefile > astral/cycad.genetrees.tre
astral -i cycad.genetrees.tre -o cycad.astral.tre
```

## ToDo

### Rerun without the definitely bad samples
exon and supercontig

### Population Genomics: Encephalartos horrida and Cycas platyphylla
Just need the SNP diversity, heterozygosity, Ne, for 10-15 individuals, 5 per populations
