<commit_before>#### from unbuntu 16.04 using filtered reads

```
docker pull quay.io/biocontainers/megahit:1.1.1--py36_0
docker pull quay.io/biocontainers/quast:4.5--boost1.61_1
docker pull quay.io/biocontainers/prokka:1.11--0
```

#link the data and Megahit
```
docker run -v /home/ubuntu/data:/data -it quay.io/biocontainers/megahit:1.1.1--py36_0 megahit --12 /data/SRR606249_subset10.pe.trim.fq.gz -o /data/podar_metaG_sub_10
```
Now run quast to generate some assembly statistics 
```
docker run -v /home/ubuntu/data:/data -it quay.io/biocontainers/quast:4.5--boost1.61_1 quast.py /data/podar_metaG_sub_10/final.contigs.fa -o /data/podar_metaG_sub_10_quast_report
```

Now annotate your contigs with prokka
```
docker run -v /home/ubuntu/data:/data -it quay.io/biocontainers/prokka:1.11--0 prokka /data/podar_metaG_sub_10/final.contigs.fa --outdir /data/prokka_annotation --prefix podar_metaG_sub_10 
```
<commit_msg>updated language <commit_after>#### from unbuntu 16.04 using filtered reads

```
docker pull quay.io/biocontainers/megahit:1.1.1--py36_0
docker pull quay.io/biocontainers/quast:4.5--boost1.61_1
docker pull quay.io/biocontainers/prokka:1.11--0
```

#link the data and run Megahit
```
docker run -v /home/ubuntu/data:/data -it quay.io/biocontainers/megahit:1.1.1--py36_0 megahit --12 /data/SRR606249_subset10.pe.trim.fq.gz -o /data/podar_metaG_sub_10
```
Now run quast to generate some assembly statistics 
```
docker run -v /home/ubuntu/data:/data -it quay.io/biocontainers/quast:4.5--boost1.61_1 quast.py /data/podar_metaG_sub_10/final.contigs.fa -o /data/podar_metaG_sub_10_quast_report
```
Now annotate your contigs with prokka
```
docker run -v /home/ubuntu/data:/data -it quay.io/biocontainers/prokka:1.11--0 prokka /data/podar_metaG_sub_10/final.contigs.fa --outdir /data/prokka_annotation --prefix podar_metaG_sub_10 
```

{'fraction_non_alphanumeric': 0.1416982152514873, 'fraction_numerical': 0.06057328285559762, 'mean_word_length': 4.36231884057971, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4288409', 'n_tokens_mistral': 858, 'n_tokens_neox': 761, 'n_words': 139}