/usr/share/doc/seqsero/README.md is in seqsero 1.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | # SeqSero 1.0
Salmonella serotyping from genome sequencing data
# Introduction
SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. A web app is available at www.denglab.info/SeqSero
# Dependencies
SeqSero depends on:
1. Python 2.7 and [Biopython 1.65](http://biopython.org/wiki/Download);
2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/);
3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/);
4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
5. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);
6. [isPcr](http://hgwdev.cse.ucsc.edu/~kent/exe/linux/) written by Jim Kent.
# Executing the code
Usage: SeqSero.py
-m <int> (input data type, '1' for interleaved paired-end reads , '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly)
-i <file> (/path/to/input/file)
-b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional)
# Output
Upon executing the command, a directory named 'SeqSero_result_<time_you_run_SeqSero>' will be created. Your result will be stored in 'Seqsero_result.txt' in that directory
# Citation
Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
Salmonella serotype determination utilizing high-throughput genome sequencing data.
**J Clin Microbiol.** 2015 May;53(5):1685-92.[PMID:25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)
|