Btrim is a fast and lightweight tool to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. Two Linux executables can be downloaded: Btrim32 for 32-bit machine, and Btrim64 for 64-bit machine. If the program does not run on your Linux machine, try btrim32-static or btrim64-static. An executable for Mac (btrim_mac) can also be downloaded. Options: Btrim -q -p -t -o [-u 5'-error -v 3'-error -l minlen -b <5'-cut> -e <3'-cut> -w -a -f <5'-trim> -I] Required for pattern trimming: -p each line contains one pair of 5'- and 3'-adaptors; ignored if -q in effect -t fastq file to be trimmed -o fastq file of trimmed sequences Required for quality trimming (-q in effect): -t fastq file to be trimmed -o fastq file of trimmed sequences Optional: -q toggle to quality trimming [default=adaptor trimming] -3 3'-adaptor trimming only [default=off] -P pass if no adaptor is found [default=off] -Q do a quality trimming even if adaptor is found [default=off] -s detailed trimming info for each sequence -u <5'-error> maximum number of errors in 5'-adaptor [default=3] -v <3'-error> maximum number of errors in 3'-adaptor [default=4] -l minimal insert size [default=25] -b <5'-range> the length of sequence to look for 5'-adaptor at the beginning of the sequence [default=1.3 x adaptor length] -e <3'-range> the starting position to look for 3'-adaptor at the end of the sequence [default: the 5'-trimming point] -w size of moving window for quality trimming [default=5] -a cutoff for average quality scores within the moving window for quality trimming [default=15] -f <5'-trim> number of bases to be trimmed at 5'-end [default=0] -I toggle to case sensitive search [default=case insensitive] -c toggle to check fastq file [default=no check] -S toggle to Sanger fastq format [default=Illumina] -B barcode assignment Examples: (1) Btrim64 -t input_sequence.txt -p adapters.txt -o output.txt Trim FASTQ file "input_sequence.txt" using the adapters in "adapters.txt", write the output in "output.txt". Each line in "adapters.txt" contains two tab-delimited columns: the first is 5'-adapter, the second 3'-adapter. (2) Btrim64 -p adapters.txt -t s_1_sequence.txt -o s_1.out -s s_1.sum -P -3 -Q -v 1 Trim FASTQ file "s_1_sequence.txt" using the adapters in "adapters.txt", write the output in "s_1.out" and detailed trimming information in "s_1.sum". Only 3'-adaptor will be used (the 5'-adapter in "adapters.txt" are ignored), and the maximum number of errors in 3'-adaptor is set as 1. No matter whether the adapters are found or not, the read is passed to quality trimming (-P -Q). Yong Kong Yale University Reference: Kong, Y (2011) Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies, Genomics, 98, 152-153. http://dx.doi.org/10.1016/j.ygeno.2011.05.009 Contact: yong.kong@yale.edu