Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/audy/stitch
Overlap assembler of paired-end DNA sequences generated by Illumina
https://github.com/audy/stitch
Last synced: 12 days ago
JSON representation
Overlap assembler of paired-end DNA sequences generated by Illumina
- Host: GitHub
- URL: https://github.com/audy/stitch
- Owner: audy
- License: mit
- Created: 2010-04-06T18:59:22.000Z (over 14 years ago)
- Default Branch: master
- Last Pushed: 2016-09-02T06:38:07.000Z (about 8 years ago)
- Last Synced: 2024-10-28T05:13:08.669Z (23 days ago)
- Language: Python
- Homepage:
- Size: 165 KB
- Stars: 21
- Watchers: 4
- Forks: 7
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
# Stitch
**No longer maintained**. Please use [Pandsaseq](https://github.com/neufeld/pandaseq).
Austin G. Davis-Richardson
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 `-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 MIT open source license. See `LICENSE.md` for
details.
# Citing Stitch
Please us the following citation:
Brown, Christopher T., et al. "Gut microbiome metagenomics analysis suggests a
functional model for the development of autoimmunity for type 1 diabetes." PloS
one 6.10 (2011): e25792.
Or, in BibTex:
```
@article{brown2011gut,
title={Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes},
author={Brown, Christopher T and Davis-Richardson, Austin G and Giongo, Adriana and Gano, Kelsey A and Crabb, David B and Mukherjee, Nabanita and Casella, George and Drew, Jennifer C and Ilonen, Jorma and Knip, Mikael and others},
journal={PloS one},
volume={6},
number={10},
pages={e25792},
year={2011},
publisher={Public Library of Science}
}
```
## Requirements
- Python 2.6, 2.7
- Mac OS X or Linux (Windows might work but hasn't been tested)
## Alignment Algorithm
Stitch aligns overlapping paired end reads by counting the number of matching
nucleotides in an overlapping window. The window that provides the highest
number of matching nucleotides wins.
The consensus sequence is generated thusly,
A 5' =============== =================================> 3'
B 3' <================================= =========== 5'
C 5' =============== ================================= ===========> 3'
<--------- "the middle" ---------->
In the region dubbed "the middle", the nucleotide with the highest
corresponding quality score is used (if there is a mismatch). If there is a
match, then that nucleotide is used (and the highest quality score is given).
In the case of a tie, a 'N' is used and the quality score is unchanged.
Stitch assumes that read A is 3'-5' and read B is 5'-3'. So read B is
automatically reverse-complemented in the alignment procedure. (I know I should
make this an option but I haven't yet).
## Usage
**NOTE** - Stitch expects reads to be of the same length!
Invoke, _comme ca_
Usage: stitch.py -i -j -o
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
## Bugs/Feature requests
- If you have any, [let me know](https://github.com/audy/stitch/issues). Thx!