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    (echo -e "#item\tN50\tSum\tCount" && cat) |
    mlr --itsv --omd cat

# depths
for F in ${ARRAY[@]}; do
    fasr subset <(echo S288c) ${F} --required |
        grep '^>S288c.' |
        spanr cover stdin |
        spanr stat --all S288c/chr.sizes stdin |
        sed '1d' |
        tr ',' '\t' |
        sed "s/^/${F}\t/"

    # single copy
    fasr subset <(echo S288c) ${F} --required |
        grep '^>S288c.' |
        spanr coverage -d stdin `# detailed depths` |
        jq '."1"' `# depth 1` |
        spanr stat --all S288c/chr.sizes stdin |
        sed '1d' |
        tr ',' '\t' |
        sed "s/^/${F}\t/"
done |
    (echo -e "#item\tchrLength\tsize\tcoverage" && cat) |
    mlr --itsv --omd cat

fasr subset <(echo S288c) S288cvsRM11_1a_lpcnam_axt.fas --required |
    grep '^>S288c.' |
    spanr coverage -d stdin


```

| #item                         | N50   | Sum      | Count |
|-------------------------------|-------|----------|-------|
| S288cvsRM11_1a_lav2axt.fas    | 84580 | 12603461 | 821   |
| S288cvsRM11_1a_lpcnam_axt.fas | 81344 | 11578920 | 307   |
| S288cvsRM11_1a_lpcnam_syn.fas | 83326 | 11455734 | 257   |
| S288cvsRM11_1a_partition.fas  | 77565 | 11579491 | 327   |

| #item                         | chrLength | size     | coverage |
|-------------------------------|-----------|----------|----------|
| S288cvsRM11_1a_lav2axt.fas    | 12071326  | 11627698 | 0.9632   |
| S288cvsRM11_1a_lav2axt.fas    | 12071326  | 11038024 | 0.9144   |
| S288cvsRM11_1a_lpcnam_axt.fas | 12071326  | 11578920 | 0.9592   |
| S288cvsRM11_1a_lpcnam_axt.fas | 12071326  | 11578920 | 0.9592   |
| S288cvsRM11_1a_lpcnam_syn.fas | 12071326  | 11455734 | 0.9490   |
| S288cvsRM11_1a_lpcnam_syn.fas | 12071326  | 11455734 | 0.9490   |
| S288cvsRM11_1a_partition.fas  | 12071326  | 11579491 | 0.9593   |
| S288cvsRM11_1a_partition.fas  | 12071326  | 11579491 | 0.9593   |

### A quick dotplot

```shell
cd ~/data/egaz

brew install wang-q/tap/wfmash
cargo install --git https://github.com/ekg/pafplot --branch main

wfmash S288c/chr.fasta RM11_1a/chr.fasta > aln.paf
paf2dotplot png medium aln.paf

pafplot aln.paf

```

## Template steps

```shell script
cd ~/data/egaz

egaz template \
    S288c RM11_1a YJM789 Spar Spas Seub \
    --multi -o multi6/ \
    --mash --fasttree --parallel 6 -v

bash multi6/1_pair.sh
bash multi6/2_mash.sh
bash multi6/3_multi.sh

egaz template \
    S288c RM11_1a YJM789 Spar \
    --multi -o multi6/ \
    --multiname multi4 --tree multi6/Results/multi6.ft.nwk \
    --outgroup Spar \
    --vcf \
    --fasttree --parallel 6 -v

bash multi6/3_multi.sh
bash multi6/4_vcf.sh
bash multi6/9_pack_up.sh

```