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Clean the Sequencie
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Clean the Sequencie
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### Start download the Univec (dataset its a fasta file with contaminants, vectors, adaptors to remove) and Seqclean (programm)
$ wget
$ wget https://github.com/ibest/seqyclean/archive/refs/tags/1.10.09.tar.gz
### unzip the archive > 1.10.09.tar.gz
$ tar xfvz 1.10.09.tar.gz
$ cd seqyclean-1.10.09/
$ make
### the command make is from the tutorial
$ cd bin
$ ls
$ seqyclean
### The archive will use to clean
### start to clean the sequencies
### I start the command-c = Turns on contaminants screening, default=off, <filename> - is a path to a FASTA-file containing contaminant genomes from UniVec
### Using the argument -U <filename> = Single-end mode (as you can see in seqyclean tutorial)
### -o to send the new archive to
$ /home/usuary_name/directory_name/seqyclean-1.10.09/bin/seqyclean -U archive_name -c /home/usuary_name/directory_name/UniVec -minlen 50 -qual 24 24 -o /home/usuary_name/directory_name/folder_name/new_archive_name
### Basically you have the path of the program you use (/home/usuary_name/directory_name/seqyclean-1.10.09/bin/seqyclean) the name of archive you will use in the programm (-U archive_name)
### -o and the path you would like to copy (/home/usuary_name/directory_name/folder_name/new_archive_name)
### I change to command -v = Turns on vector trimming, default=off. <filename> - is a path to a FASTA-file containing vector genomes.
$ /home/usuary_name/directory_name/seqyclean-1.10.09/bin/seqyclean -U archive_name -v /home/usuary_name/directory_name/UniVec -minlen 50 -qual 24 24 -o /home/usuary_name/directory_name/folder_name/new_archive_name
### after doing with all the archives... start to make fastq analisys
$