... | ... | @@ -399,7 +399,7 @@ sed -i 's/=[^=]*//2g' envs/flye_v2_7.yaml |
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```
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################################
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##### Checkpoint Snakefile #####
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###############################
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################################
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cp updated_SNAKEFILE checkpoint_SNAKEFILE
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# edited the paths to the 'rules' and 'workflows' in the "checkpoint_SNAKEFILE", to include the above files
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# test run the "checkpoint_SNAKEILF"
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... | ... | @@ -437,7 +437,7 @@ cp prepare_plot_files.sh [prepare_plot_files_w_metaspades.sh](https://git-r3lab. |
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```
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|
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##### CD-HIT #####
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- comparing metaspades_sr and metaspades_hybrid proteins to see which contributes more to the mmseq comparisons
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- Using [cd-hit](https://github.com/weizhongli/cdhit) compared metaspades_sr and metaspades_hybrid proteins to see which contributes more to the mmseq comparisons
|
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|
```
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cd /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB
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mkdir cd-hit && cd cd-hit
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... | ... | @@ -599,14 +599,14 @@ cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/ |
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mkdir circular
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cd circular
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conda activate circlator
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conda install canu
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conda activate [circlator](https://github.com/sanger-pathogens/circlator)
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conda install [canu](https://github.com/marbl/canu)
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circlator all ../results/assembly/flye/lr/merged/barcode07/assembly.fna ../results/basecalled/merged/barcode07.fna flye_circlator_output
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# failing in 10-hour interactive so submitted as bash script
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sbatch -p bigmem -t 2-00:00:00 -N 1 -n 24 run_circlator.sh (OR) sbatch -p bigmem -t 0-16:00:00 -N 1 -n 24 run_circlator.sh # failed after a while, so going to manual methods below
|
|
|
|
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# Checking graph with Bandage
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|
|
# Checking graph with [Bandage](https://github.com/rrwick/Bandage)
|
|
|
conda activate bandage
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|
|
Bandage info ../results/assembly/metaspades_hybrid/lr_barcode07-sr_NEB2_MG_S17/assembly_graph_with_scaffolds.gfa
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|
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|
... | ... | @@ -619,7 +619,7 @@ ml bio/BioPerl/1.7.1-foss-2017a-Perl-5.24.1 |
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perl -0076 -ne ‘{chomp; m/(.*):(.*);/; print “>$_” if $1 ne $2};’ < /scratch/users/sbusi/ONT/cedric_ont_basecalling/results/assembly/metaspades_hybrid/lr_barcode07-sr_NEB2_MG_S17/assembly_graph.fastg > megahit_singleton_removed.fastg
|
|
|
```
|
|
|
|
|
|
##### GraphBin #####
|
|
|
##### [GraphBin](https://github.com/Vini2/GraphBin) #####
|
|
|
- https://github.com/Vini2/GraphBin - for binning from graphs
|
|
|
- downloaded the "methylation-aware" flye assembly and .gfa files to desktop
|
|
|
- also downloaded the flye_maxbin_scaffolds2bin.tsv and saved as .csv
|
... | ... | @@ -646,7 +646,7 @@ python graphbin.py --assembler spades --graph spades_input/assembly_graph_with_s |
|
|
```
|
|
|
|
|
|
##### AGB #####
|
|
|
- Trying AGB: https://almiheenko.github.io/AGB/manual.html
|
|
|
- Trying [AGB](https://almiheenko.github.io/AGB/manual.html) for circularity analyses
|
|
|
```
|
|
|
cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB
|
|
|
conda create -c almiheenko -c bioconda -n AGB agb
|
... | ... | |