Length Filter a Fasta

Have you ever wanted to get the sequences in your fasta file that are longer than a certain length?  Try this short script:

Alignment with Bowtie (and Bowtie2)

For those who only know a bow tie as something worn by hipsters or really fancy people — Bowtie is a very powerful bioinformatics tool that has a diverse array of applications. ┬áMost often I will use Bowtie to map RNA transcripts back to a known genome; however, you can also use Bowtie to assess how well your assembly performed or for any instance where you want to find how many of your high throughput sequences map back to a [longer] sequence or genomes of interest.

What makes Bowtie special is that it requires little RAM (can easily run on your laptop) and is very fast — or as the creators of Bowtie declare: ultrafast (aligning more than 25 million reads to the human genome in 1 CPU hour) . Continue reading