ONT_pilot_w_GDB_samples.md

@@ -399,7 +399,7 @@ sed -i 's/=[^=]*//2g' envs/flye_v2_7.yaml
 ```
 ################################
 ##### Checkpoint Snakefile #####
-###############################
+################################
 cp updated_SNAKEFILE checkpoint_SNAKEFILE
 # edited the paths to the 'rules' and 'workflows' in the "checkpoint_SNAKEFILE", to include the above files 
 # test run the "checkpoint_SNAKEILF"
@@ -437,7 +437,7 @@ cp prepare_plot_files.sh [prepare_plot_files_w_metaspades.sh](https://git-r3lab.
 ```
 
 ##### CD-HIT #####
-- comparing metaspades_sr and metaspades_hybrid proteins to see which contributes more to the mmseq comparisons
+- Using [cd-hit](https://github.com/weizhongli/cdhit) compared metaspades_sr and metaspades_hybrid proteins to see which contributes more to the mmseq comparisons
 ```
 cd /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB
 mkdir cd-hit && cd cd-hit
@@ -599,14 +599,14 @@ cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/
 mkdir circular
 cd circular
 
-conda activate circlator
-conda install canu
+conda activate [circlator](https://github.com/sanger-pathogens/circlator)
+conda install [canu](https://github.com/marbl/canu)
 circlator all ../results/assembly/flye/lr/merged/barcode07/assembly.fna ../results/basecalled/merged/barcode07.fna flye_circlator_output
 
 # failing in 10-hour interactive so submitted as bash script
 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
 
-# Checking graph with Bandage
+# Checking graph with [Bandage](https://github.com/rrwick/Bandage)
 conda activate bandage
 Bandage info ../results/assembly/metaspades_hybrid/lr_barcode07-sr_NEB2_MG_S17/assembly_graph_with_scaffolds.gfa
 
@@ -619,7 +619,7 @@ ml bio/BioPerl/1.7.1-foss-2017a-Perl-5.24.1
 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