Recently, NCBI released their new datasets API that might replace NCBI E-utils. At the moment, datasets is focused on genomes, genes, and viruses, but no doubt it will expand over time. [As an aside: I think the name is terrible, and they should use ncbi_datasets (see this tweet)]

Here is a rough guide to extracting some data about genomes using datasets.

Python has a versioning module that will automatically get its version from your latest git tag, and put that version in a pip repository.

Briefly, here are the components

Here are some (probably simple) mmseqs2 tips that you probably don’t remember how to do. If you need explanations or details, read the mmseqs2 wiki. Otherwise, good luck!

We often want to calculate Pearson correlation between different datasets, for example, we have used it to identify the hosts of different phages. Often, we want to calculate Pearson on really large matrices, and so our usual solution is to use crappy code and be patient!

However, recently Daniel Jones released turbocor, a fast, rust-based implementation, of pairwise Pearson correlations, and so we are intrigued to work with it. Here is a brief guide to making correlations using turbocor.

Here are some tips and tricks for minimap2 that I keep forgetting!

–split-prefix

If you have a large (>4 GB) multisequence index file, there are two options.

The first is to increase the value of -I when you build the index (preferred) so that the whole index is kept in memory. Note: This must be done when you build the index, you can’t build the index and then change -I during runtime.

The second is to use --split-prefix with a string. For snakemake, there are two options:

1. You can use "{sample}" as your prefix like so:

params:
    prfx = "{sample}"
...
shell:
    """
         minimap2 --split-prefix {params.prfx} ...
    """

2. You can use a random 6 character string like so:

import random, string

params:
        pfx = ''.join(random.choices(string.ascii_uppercase + string.digits, k=6)) 
...
shell:
    """
         minimap2 --split-prefix {params.prfx} ...
    """

The trick is here, things will probably break if your index file is small. If you see the errorr: [W::sam_hdr_create] Duplicated sequence it is probably because you have split a small index sequence, and the sequence IDs are being duplicated. Remove the --split-prefix option and you should be good.

A few tips and tricks for working with slurm (i.e. submitting jobs using sbatch) that I frequently forget!

We use Google Scholar a lot to search the literature, but also to track our own works. Several grant administration systems use ORCID to retrieve citations. Here is how you can “easily” update ORCID with all your citations from Google Scholar.