Bacsort
Bacsort copied to clipboard
rrwick
a collection of scripts for organising bacterial genomes by species
combine_distance_matrices.py script does not work with numpy version 1.12 - I had to updated to 1.14 and then it worked for me. Might be worth flagging this in the README....
Hi Ryan, After running fastANI and getting some blank outputs I was confused as the fastANI scripts were suggesting that the job was actually being run. Later I realised I...
Hi I use fastANI distance matrix, first converted to fastani.phylip using following code, ``` pairwise_identities_to_distance_matrix.py --max_dist 0.2 tree/fastani_output > tree/fastani.phylip ``` then creates a tree with ``` bionj_tree.R tree/distances.phylip tree/tree.newic...
Hi I use bionj_tree.R created a phylogeny tree. However, the tree has no branches length information. Is there a way to add branches length to the tree? Also, I don't...
Dear Ryan, thanks for developing Bacsort. I'm trying to run it on a bunch of genomes from isolates and cluster_genera.py fails every time, but I can't interpret the error. Do...
Hello, I have a .matrix file from FastANI results. I really don't want to run Mash. I just to convert the .matrix file to a newick tree asap. Let me...
Hi, When I run: `download_genomes.sh "Methanosarcina"` It gives me: `find: refseq/bacteria: No such file or directory` Any tips on downloading from an archaeal genus? Many thanks! Gaofeng
I installed appdirs using pip (followed the installation guide), but ran into multiple errors. `(base) steve@steve-VM:~/Documenten/bacsort_results$ download_genomes.sh Salmonella Checking for Mash ------------------------------------------------ /home/steve/anaconda3/bin/mash Mash found! Checking grep... good Downloading genomes...
Hi, First thank for this vital (now for me) tool. I only used it to the genus clade of Klebsiella. I propose to add (only justified by a tree analysis)...
