A simple and quick tool to read huge FastQ and FastA files (both normal and gzipped) and manipulate them.
It makes use of the KSeq library (http://lh3lh3.users.sourceforge.net/kseq.shtml) for fast access to FastQ/A files.
Clone this repository and run make.
Usage: %s (--rev) (--append [string_to_append_to_header]) (--to-fasta) (--illumina-trinity) sequences_1.fastq/a sequences_2.fastq/a ...
--to-fasta (optional): convert FastQ files to FastA format.
--rev (optional): reverse complement all the sequences in the dataset (both FastQ and FastA).
--append (optional): add a string at the end of each sequence header (both FastQ and FastA).
--illumina-trinity (optional): directly converts Casava 1.8+ FastQ ID format to Trinity Fasta input format (appending /1 and /2 for PE reads)
FastQ conversion for Trinity pipeline
fastool --illumina-trinity sequences.fastq > sequences.fasta
FastQ to FastA conversion
fastool --to-fasta sequences.fastq > sequences.fasta
Return the reverse complement
fastool --rev sequences.fastq > reverse_complement.fastq
Append '/1' to the end of the sequence ID
fastool --append /1 sequences.fasta > forward_sequences.fasta
Append '/2' to the end of the sequence ID and return the reverse complement
fastool --append /2 --rev sequences.fasta > reverse_sequences.fasta
Can process more then one file
fastool --to-fasta --append /1 sequences1.fastq sequences2.fastq sequences3.fastq > all_sequences.fasta
Can be used with pipes, for example to read from compressed files
zcat sequences.fastq.gz | fastool --to-fasta > sequences.fasta
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Copyright (c) 2012 Francesco Strozzi