sequence_processing

some scripts to process fasta and fastq sequences

remove duplicates

This script takes a fasta file from STDIN, removes duplicated sequences and writes the output to STDOUT.

Sequences will be deleted, if they have an identical header and an identical sequence. This script can also clean the fasta file: Linebreaks in the sequence as well as empty lines and leading whitespaces in headers (> id) are removed by default. Additionally, non ACGT charachters are converted to N. This feature can be skipped using the –no-convert option. The script also converts lowercase sequence characters to uppercase. This can be skipped with the –no-up option.

Use one the following commands for help:

./remove_dulicates --help
perldoc ./remove_duplicates

sample from fasta

This script takes a fasta file and a number of sequences (n) to sample. It writes n randomly selected sequences to the output file.

This script can also clean the fasta file: Linebreaks in the sequence as well as empty lines and leading whitespaces in headers (> id) are removed by default. Additionally, non ACGT charachters can be converted to N and lowercase sequence characters can be converted to uppercase.

Use the following command for help:

./sample_from_fasta.pl --help

split fasta

This script takes a fasta file and generates a new file for each sequence. The new files are named as <input.fa>.sequenceID

This script will also clean the fasta file: Linebreaks in the sequence as well as empty lines and leading whitespaces in headers (> id) are removed by default. Additionally, non ACGT charachters can be converted to N and lowercase sequence characters can be converted to uppercase.

Use the following command for help:

./sample_from_fasta.pl --help