Extract sequence subset

How to extract or remove sequences from fasta or fastq file

1) Using seqtk

# get a list of all sequence IDs

# example: get all geneIDs from a fasta file

cat genes.fasta | grep '>' | cut -f 1 -d ' ' | sed 's/>//g' > list_of_geneIDs.txt

# get subset IDs: create a text-file with selected sequence IDs

# Example: select top 3 genes as subset

head -3 list_of_geneIDs.txt > subsetIDs.txt

gene_001

gene_002

gene_003

# extract subset of gene sequences based on list of sequence IDs in .txt file

seqtk subseq genes.fasta subsetIDs.txt > gene_subset.fasta

# install Seqtk (Linux/Ubuntu)

sudo apt-get install seqtk