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1 # SeqSero2 v1.1.0
2 Salmonella serotype prediction from genome sequencing data.
3
4 Online version: http://www.denglab.info/SeqSero2
5
6 # Introduction
7 SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies
8
9 # Dependencies
10 SeqSero2 has three workflows:
11
12 (A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing).
13
14 Allele micro-assembly workflow depends on:
15
16 1. Python 3;
17
18 2. Biopython 1.73;
19
20 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/);
21
22 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/);
23
24 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
25
26 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);
27
28 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades);
29
30 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/);
31
32 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID).
33
34
35 (B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants.
36
37 Raw reads k-mer workflow (originally SeqSeroK) depends on:
38
39 1. Python 3;
40 2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files);
41
42
43 (C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow
44
45 # Installation
46 ### Conda
47 To install the latest SeqSero2 Conda package (recommended):
48 ```
49 conda install -c bioconda seqsero2=1.1.0
50 ```
51 ### Git
52 To install the SeqSero2 git repository locally:
53 ```
54 git clone https://github.com/denglab/SeqSero2.git
55 cd SeqSero2
56 python3 -m pip install --user .
57 ```
58 ### Other options
59 Third party SeqSero2 installations (may not be the latest version of SeqSero2): \
60 https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \
61 https://github.com/denglab/SeqSero2/issues/13
62
63
64 # Executing the code
65 Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions.
66
67 Usage: SeqSero2_package.py
68
69 -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a)
70
71 -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq)
72
73 -i <file> (/path/to/input/file)
74
75 -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1)
76
77 -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode)
78
79 -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number)
80
81 -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files)
82
83 -n <string> (optional, to specify a sample name in the report output)
84
85 -s <flag> (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv)
86
87 --check <flag> (use '--check' flag to check the required dependencies)
88
89 -v, --version (show program's version number and exit)
90
91
92 # Examples
93 Allele mode:
94
95 # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10")
96 SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz
97
98 K-mer mode:
99
100 # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2")
101 SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz
102
103 # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k")
104 SeqSero2_package.py -m k -t 4 -i assembly.fasta
105
106 # Output
107 Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode).
108
109
110 # Citation
111 Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X.
112 SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.
113 **Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long)
114
115 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
116 Salmonella serotype determination utilizing high-throughput genome sequencing data.
117 **J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)