cutadapt has more parameters
fastx is not pair-safe - it will discard sequences that are "all-adapter" which screws up the pairing
the fastx clipper is much more aggressive than cutadapt or scythe using default parameters, for example:
$ cat sample.fq
@HWI-ST431_52:1:1:1259:1981/1
GTTCAGAGTTCTACAGTCCGACAATCGTATGCCGTNTTCTGCTTGAAAAAANNNANAANNNNANNTNNNNNGNGNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
b`ZUYZKYUSV[[_[cad\\W\[X`ddadc^``^ZB][]\Tc\^`ccbdbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
fastx:
$ fastx_clipper -a ATCTCGTATGCCGTCTTCTGCTTG -i sample.fq
@HWI-ST431_52:1:1:1259:1981/1
GTTCAGAGTTCTACAGTCCGA
+
b`ZUYZKYUSV[[_[cad\\W
cutadapt:
$ cutadapt -a ATCTCGTATGCCGTCTTCTGCTTG sample.fq
@HWI-ST431_52:1:1:1259:1981/1
GTTCAGAGTTCTACAGTCCGACAATCGTATGCCGTNTTCTGCTTGAAAAAANNNANAANNNNANNTNNNNNGNGNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
b`ZUYZKYUSV[[_[cad\\W\[X`ddadc^``^ZB][]\Tc\^`ccbdbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
scythe:
$ scythe -a adapter.fa sample.fq
@HWI-ST431_52:1:1:1259:1981/1
GTTCAGAGTTCTACAGTCCGACAATCGTATGCCGTNTTCTGCTTGAAAAAANNNANAANNNNANNTNNNNNGNGNNNNNNNNNNNNNNNNNNNNNNNNNNN
+HWI-ST431_52:1:1:1259:1981/1
b`ZUYZKYUSV[[_[cad\\W\[X`ddadc^``^ZB][]\Tc\^`ccbdbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
trimmomatic
$trimmomatic SE sample.fq sample.out ILLUMINACLIP:adapter.fa:2:30:10
TrimmomaticSE: Started with arguments:
sample.fq sample.out ILLUMINACLIP:adapter.fa:2:30:10
Automatically using 2 threads
Using Long Clipping Sequence: 'ATCTCGTATGCCGTCTTCTGCTTG'
ILLUMINACLIP: Using 0 prefix pairs, 1 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred64
Input Reads: 1 Surviving: 1 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully
$ more sample.out
@HWI-ST431_52:1:1:1259:1981/1
GTTCAGAGTTCTACAGTCCGA
+
b`ZUYZKYUSV[[_[cad\\W
fastp
$ fastp -i sample.fq -n 50 -a ATCTCGTATGCCGTCTTCTGCTTG --stdout
Streaming uncompressed output to STDOUT...
@HWI-ST431_52:1:1:1259:1981/1
GTTCAGAGTTCTACAGTCCGACAATCGTATGCCGTNTTCTGCTTGAAAAAANNNANAANNNNANNTNNNNNGNGNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
bZUYZKYUSV[[_[cad\\W\[X
ddadc^`^ZB][]\Tc\^
ccbdbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
Also consider find_adaptor: http://code.google.com/p/biopieces/wiki/find_adaptor
and consider: https://github.com/ucdavis-bioinformatics/scythe
@maasha: Thanks, I haven't stumbled on biopieces before ... looks interesting!