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Commit 01c91efe authored by james94's avatar james94
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containerization

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......@@ -22,20 +22,31 @@
1. [**Build** meryl k-mer databases](#build-meryl-k-mer-databases)
- Requires: WGS sequencing libraries (Pacbio HiFi or Illumina PE short-insert `.fastq`'s)
- Output: (`.meryl`) k-mer database
<br>
![](https://i.imgur.com/HK4ZMi2.png)
- Requires: WGS sequencing libraries (Pacbio HiFi or Illumina PE short-insert `.fastq`'s)
- Output: (`.meryl`) k-mer database
<br>
2. [Assembly **Evaluation**](#assembly-evaluation)
- Requires: (`.meryl`) k-mer databases and corresponding genome assemblies (`.fasta`'s) you wish to evaluate. As well as HiC Libraries as optional input.
- Output:
- Assembly Stats (L#, N#, Scaffold, contig, etc.)
- BUSCO results
- QV Score
- K-mer Completeness
- genomescope profile
- Pretext Map (optional)
- **PDF Report aggregating all of the above**
<br>
![](https://i.imgur.com/8eLKPtK.png)
- Requires: (`.meryl`) k-mer databases and corresponding genome assemblies (`.fasta`'s) you wish to evaluate. As well as HiC Libraries as optional input.
- Output:
- Assembly Stats (L#, N#, Scaffold, contig, etc.)
- BUSCO results
- QV Score
- K-mer Completeness
- genomescope profile
- Pretext Map (optional)
- **PDF Report aggregating all of the above**
![](https://i.imgur.com/hWMo4PF.png)
......
......@@ -4,10 +4,7 @@ channels:
- bioconda
- anaconda
dependencies:
- snakemake==6.6.1
- python>=3.9.10
- tabulate=0.8.7
- snakemake==7.3.8
- beautifulsoup4=4.9
- mamba=0.15.2
- pandoc=2.15.*
- tectonic
- pandas
- numpy
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