library(dada2)

read_f <- "10_1.fastq.gz"
read_r <- "10_2.fastq.gz"
filt_f <- "10_1_filt.fastq.gz"
filt_r <- "10_2_filt.fastq.gz"
filt_f_b <- "10_1_filt_b.fastq.gz"
filt_r_b <- "10_2_filt_b.fastq.gz"

trunc_len <- 250
trunc_q <- 2
max_ee <- 20
rm_lowcomplex <- 15

ff <- filterAndTrim(read_f, filt_f,
    truncLen = trunc_len,
    truncQ = trunc_q,
    maxEE = max_ee,
    rm.lowcomplex = rm_lowcomplex,
)
fr <- filterAndTrim(read_r, filt_r,
    truncLen = trunc_len,
    truncQ = trunc_q,
    maxEE = max_ee,
    rm.lowcomplex = rm_lowcomplex,
)
fb <- filterAndTrim(read_f, filt_f_b, read_r, filt_r_b,
    truncLen = trunc_len,
    truncQ = trunc_q,
    maxEE = max_ee,
    rm.lowcomplex = rm_lowcomplex,
)

ff
#               reads.in reads.out
# 10_1.fastq.gz   146725     86619

fr
#               reads.in reads.out
# 10_2.fastq.gz   146725     23538

fb
#               reads.in reads.out
# 10_1.fastq.gz   146725     86348