# AddAdapters Guide

Written by Brian Bushnell  
Last updated December 22, 2015

**AddAdapters** is designed for grading the performance of adapter-trimming tools. It can add adapters to reads, and annotate the reads with their correct post-trimming length; and it can be run on trimmed reads, to calculate the rates of correct and incorrect trimming. However, it does not understand insert size, so for adding adapters to paired reads, it's better to use **RandomReads**. As such, this is *deprecated for paired reads*.

## Usage Examples

### To add adapters to reads:

```bash
addadapters.sh in=a.fq out=b.fq adapters=adapters.fa
```

### To grade trimmed reads:

```bash
addadapters.sh in=trimmed.fq grade
```

### To use RandomReads instead, to add adapters in the correct location according to insert size:

```bash
randomreads.sh ref=ref.fa out=reads.fq len=150 paired reads=100k mininsert=50 maxinsert=350 fragadapter1=ACTG fragadapter2=ACTG
rename.sh in=reads.fq out=renamed.fq renamebytrim interleaved
```

The result of this will still be named correctly for grading by **AddAdapters**. "ACTG" would normally be a much longer adapter sequence.