genomewalker

For the C program:

# Igraph C-library
wget https://igraph.org/nightly/get/c/igraph-0.7.1.tar.gz
tar xvfz igraph-0.7.1.tar.gz
cd igraph-0.7.1
./configure --prefix="${PREFIX}"/igraph/0.7.1
make -j 8
make check

genomewalker

easy-taxonomy e77760e07c3167ef94f937365175d68b.assm.combined.fasta DB/uniref50-tax/UniRef50 e77760e07c3167ef94f937365175d68b.UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50 --tax-lineage 2 --majority 0.5 --vote-mode 1 --lca-mode 3 --orf-filter 1 --lca-ranks superkingdom,phylum,class,order,family,genus --threads 32 

MMseqs Version:                        	5daca424b162cc5fdf0b9cd151aebed86975cbf6
ORF filter                             	1
ORF filter e-value                     	100
ORF filter sensitivity                 	2
LCA mode                               	3
Majority threshold                     	0.5
Vote mode                              	1
LCA ranks                              	superkingdom,phylum,class,order,family,genus

genomewalker

name: anvio-7.1
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python=3.6
  - anvio=7
  - diamond=0.9.14
  - pip

genomewalker

Sub AuthorTec_ReplaceAuthorName()

Const MacroName = "AuthorTec™ Replace Author Name"

'In XML formatted Word documents (docx, dotx, docm, dotm), this

'macro changes a specified author name on comments and tracked

'revisions. It runs on both Windows and Mac versions of Microsoft Word

genomewalker

Get the data from figshare

convert the DB into fasta

mkdir agnostos-comp cd agnostos-comp

mkdir one_step two_step

tar xvfz mg_gtdb_20190502.tar.gz ln -s mg_gtdb_db_20190502.dbtype mg_gtdb_db_20190502_h.dbtype

genomewalker

genomewalker

REMOVE JAMF RESTRICTIONS ON MAC

REMOVE ONLY RESTRICTIONS

sudo jamf removeMDMProfile removes all restrictions

sudo jamf manage brings back all restrictions and profiles

REMOVE ALL RESTRICTIONS AND DISABLE JAMF BINARIES WHILE KEEPING YOUR ACCESS TO VPN AND OTHER SERVICES

sudo jamf removeMDMProfile removes all restrictions

genomewalker

from tqdm import tqdm
from collections import defaultdict
import argparse
from concurrent.futures import ThreadPoolExecutor, as_completed
from multiprocessing import Pool
import gzip
from itertools import zip_longest
from mimetypes import guess_type
from functools import partial
from cdifflib import CSequenceMatcher

genomewalker

Diferences on bowtie2 alignment time between concatenated and non-concatenated genomes

• Concat number of references: 52,517
• No concat number of references: 8,086,857
• Number of reads: 164,369,171

# CONCAT
$ bowtie2-build --seed 42 --threads 24 genomes-concat.fa genomes-concat

...

genomewalker

library(tidyverse)

# Read in the data
setwd("/maps/projects/lundbeck/scratch/taxDB/v6/metadata/src_files")

ncbi_assm_stats <- list.files(".", pattern = "genome_metadata.txt", full.names = TRUE)
ncbi_assm_stats <- map_dfr(ncbi_assm_stats, function(X) {
    read_tsv(X, col_names = TRUE)
}) %>%
    select(-filename) %>%