Challenges in pre-processing data for Phylogenomics

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We are seeking to understand what the primary challenges are in getting phylogenomic data ready for analysis. As the developers of cogent3, a python library for genomic data wrangling and molecular evolutionary analysis, we want to know what these primary bottlenecks are. Where possible, we will develop solutions and post them as tutorials at cogent.org.

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What is your comfort with coding?

I don’t know how to write scripts

I can write my own scripts in Python

Other:

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How many samples / species do you typically analyse?

<100

100-1000

>1000

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How many alignments do you typically analyse?

<50

50-500

>1000

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What sort of hardware do you use for data pre-processing?

I use my desktop / laptop

I use a shared computer (e.g. multi-machine system, supercomputer, cloud service)

Other:

What computing environment do you use for data pre-processing?

Jupyter Notebooks

Galaxy

Google Collab

Command line tools

Other:

Do you use parallel computing for pre-processing your data?

Yes

I’d like to but don’t know how

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What is the most difficult task in getting data for phylogenomic analysis?

Getting homologs to your own data

Performing multiple sequence alignment

Filtering alignments for quality

File format conversions

Managing all the different input and output files

Making the work reproducible

Other:

What public resource(s) do you typically use for your research?

GenBank

UCSC genome browser

Ensembl

Other:

What "category" of sequences do you use?

Protein coding (DNA or RNA)

RNA

Non genic (e.g. ultra-conserved elements, introns)

If you use protein coding sequences, do you

Translate into amino acids and use those

Use the DNA sequences

Use the alignment of amino acids to get the DNA sequence alignment

Directly align using a codon aligner

I’d like to use a codon aligner but don't know how

If you perform multiple sequence alignments on your data , do you

Use default settings of the aligner program

Evaluate the impact of different aligner programs or different settings on alignment quality

I’d like to evaluate the impact of these choices but don’t know how

Other:

If you perform quality control on your alignments, do you

Check all alignments contain the same species (or some minimum number)

Check the alignments satisfy some minimum length

Remove sequences that cause too many gaps

Visually inspect randomly selected alignments

Other:

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