use seqtk to extract subsequences from FASTA files

[ctb]

a quick tutorial!

hackmd: https://hackmd.io/VYrGL_i8SA6WIALlHs16tA?view

reproduced below:

Using seqtk subseq to subselect sequences

This is a quick mini-tutorial on using seqtk to extract a set of sequences from a gzipped FASTA file; it should also work with uncompressed files and FASTQ files (compressed or not).

Installation of seqtk below requires an installation of conda & mamba; I recommend using mambaforge.

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On farm, in a datalab-XX account:

First, install seqtk in a conda environment named seq:

mamba create -y -n seq seqtk

Activate seq:

mamba activate seq

Make a new working directory:

mkdir -p ~/extract-from-fasta
cd ~/extract-from-fasta

Download a FASTA file of contigs:

curl -L https://osf.io/download/7bzrc -o contigs.fasta.gz

List names of sequences in FASAT file:

gunzip -c ^'>' contigs.fasta.gz

Make a text file containing the names of a few contigs from that file:

echo k117_180 > extract-list.txt
echo k117_181 >> extract-list.txt

:::warning
Here, the names to extract can be just the prefix of the sequence you want to extract - but the names have to match at the beginning? Not 100% sure.
:::

Extract using seqtk subseq:

seqtk subseq contigs.fasta.gz extract-list.txt > extracted-contigs.fasta

et voila!