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Pests are some of the most common crop problems, and they can come in several different forms. Insects are the most common and destructive, but mammals, like mice and raccoons, are also be considered crop pests in some areas. Birds are another example of a crop pest, since they can damage plants by eating seeds and fruits as well as by hunting for insects hidden in the plants.
Crop plants are those plants that are grown specifically for human consumption or other use. A crop pest is considered to be any type of creature that can damage a crop plant. Some of these pests may even destroy entire fields of crop plants in very short periods of time.
![Trimmomatic Crop Example Trimmomatic Crop Example](https://bbsmax.ikafan.com/static/L3Byb3h5L2h0dHAvaW1hZ2VzMjAxNS5jbmJsb2dzLmNvbS9ibG9nLzYzNTMxMi8yMDE1MDkvNjM1MzEyLTIwMTUwOTI5MDA0NjM5ODA4LTIxMTE2NDY4OTUucG5n.jpg)
Insects can often be found on the leaves, stems, and flowers of the plants. Many insects will also eat the fruits or vegetables of crop plants, but some of these crop pests can destroy the plants before they are even able to produce any fruits or vegetables. Some insects will eat nearly any type of plant, while others will only eat certain plants; cabbageworms, for instance, are often only seen in cabbage plants and other cole crops, like broccoli and mustard plants.
Examples which should be correctly handled include: SampleNameR1001.fq.gh - SampleNameR2001.fq.gz SampleName.f.fastq - SampleName.r.fastq SampleName.1.sequence.txt - SampleName.2.sequence.txt For output files, either of the following can be used: Explicity naming the 4 output files Providing a base file name using the –baseout flag, from which the 4 output files can be derived. Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application. There are two major modes of the program: Paired end mode and Single end mode.