diff --git a/README.md b/README.md index f451a9d8d2536e2347ffa9049b4df53c4b3b0c8a..4c31c13da547f9a0b143f81e89ea757670563a47 100644 --- a/README.md +++ b/README.md @@ -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> + + + +- 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> + + + +- 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** +  diff --git a/installGEP.yaml b/installGEP.yaml index a09bff16cbc5d3bbae8d2db8143f27a545132f3e..98140c09dac58bea36009bc061e1fc815a5dccfb 100644 --- a/installGEP.yaml +++ b/installGEP.yaml @@ -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