Austin Glenn Davis-Richardson
heyaudy@gmail.com
Stitch assembles overlapping paired-end reads into a single contig for each pair. This increases the read length and hopefully the quality of a de novo or reference assembly. Stitch is multi-threaded and will automatically use all cores on your system unless told otherwise. Stitch currently only reads FASTQ format. QSEQ and FASTA formats to come. Reads that are not found to overlap are dumped in a file called <prefix>-singletons and are in FASTQ format. These can then be trimmed and combined with contigs to do a de novo assembly.
Stitch is licensed under the GNU GPL v3.
Stitch is a pre-publication release meaning (a) It's still buggy (b) Be nice and cite me (c) send a message if you need to find out how.
- Python 2.6, 2.7
- Mac OSX or Linux (Windows might work but hasn't been tested)
NOTE - Stitch expects reads to be of the same length!
Invoke, comme ca
Usage: stitch.py -i <fastq file 1> -j <fastq file 2> -o <output prefix>
More options,
-h, --help show this help message and exit
-i FILEA, --first=FILEA
first fastq file
-j FILEB, --second=FILEB
second fastq file
-o PREFIX, --output=PREFIX
output prefix (omit to print to stdout)
-t THREADS, --threads=THREADS
number of threads (default = all available)
-p, --pretty_output displays overlapping contigs in a nice way.
-s SCORE, --score=SCORE
minimum percent identity (default = 25)
-b TABLE, --table=TABLE
output overlap length to a text file
- If you have any, let me know. Thx!