batch retrieval/copy the fasta sequences from the assembly file

Question

[bantony]

I have around 30,000 transcripts fasta with different contig (sequence) names. I want to pick (batch retrieval or copy) specific contigs like MK200500, MK300200, MK241000....Doing it manually would be too much time and energy spending. Is there any automatic way to batch retrieval/copy the fasta sequences given the names?

Answer 1

[GenoMax]

This is one of FAQ on Biostars. I will link one thread that has answers: Extract fasta sequences from a file using a list in another file. There are others (Retrieve a subset of FASTA from large Illumina multi-FASTA file ). This Q will likely be closed as a duplicate.