Pear is a tool to merge paired-end sequencing reads, prior to downstream tasks such as assembly.
Input: paired-end reads.
- We will use a set of Illumina MiSeq reads from the bacteria Staphylococcus aureus.
Go to your Galaxy server.
- In the tool panel, go to
Get Data: Upload File
- In the box, paste in:
Startand then Close.
- These two files will upload to your current Galaxy history.
- Using the pencil icon, change the filetype to “fastqsanger”, and shorten the name of the file.
In the tool panel, go to
Dataset type: Paired-end Name of file that contains the forward paired-end reads: ERR1712338_1.fastq Name of file that contains the reverse paired-end reads: ERR1712338_2.fastq
- Leave other settings as per defaults, except:
Maximal proportion of uncalled bases in a read: 0.01
- omits reads if >1% of the reads is missing (N)
Output files: Select all
Your tool interface should look like this:
There are four output files.
Assembled reads: merged paired-end reads. Unassembled forward readsand Unassembled reverse reads: remaining, unmerged reads. Discarded reads: Did not meet quality specified
In this case, most of the reads have been merged (~360MB); 90MB are unmerged, and 350 sequences have been discarded.
Run Trimmomatic to trim sequences before assembling.