# HG changeset patch # User cstrittmatter # Date 1587989626 14400 # Node ID b1943f530c7b8731ea52aadb08ce140d36c347c9 # Parent 3e981acf8565a8fefa6223082be2c8852f1af28f planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty diff -r 3e981acf8565 -r b1943f530c7b SeqSero2.egg-info/PKG-INFO --- a/SeqSero2.egg-info/PKG-INFO Mon Apr 27 01:31:22 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ -Metadata-Version: 1.1 -Name: SeqSero2 -Version: 1.1.0 -Summary: Salmonella serotyping -Home-page: https://github.com/denglab/SeqSero2/ -Author: Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng -Author-email: zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu -License: GPLv2 -Description: # SeqSero2 v1.1.0 - Salmonella serotype prediction from genome sequencing data. - - Online version: http://www.denglab.info/SeqSero2 - - # Introduction - SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies - - # Dependencies - SeqSero2 has three workflows: - - (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). - - Allele micro-assembly workflow depends on: - - 1. Python 3; - - 2. Biopython 1.73; - - 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); - - 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); - - 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); - - 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); - - 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); - - 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); - - 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). - - - (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. - - Raw reads k-mer workflow (originally SeqSeroK) depends on: - - 1. Python 3; - 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); - - - (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 - - # Installation - ### Conda - To install the latest SeqSero2 Conda package (recommended): - ``` - conda install -c bioconda seqsero2=1.1.0 - ``` - ### Git - To install the SeqSero2 git repository locally: - ``` - git clone https://github.com/denglab/SeqSero2.git - cd SeqSero2 - python3 -m pip install --user . - ``` - ### Other options - Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ - https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ - https://github.com/denglab/SeqSero2/issues/13 - - - # Executing the code - 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. - - Usage: SeqSero2_package.py - - -m (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) - - -t (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) - - -i (/path/to/input/file) - - -p (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) - - -b (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) - - -d (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) - - -c (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) - - -n (optional, to specify a sample name in the report output) - - -s (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) - - --check (use '--check' flag to check the required dependencies) - - -v, --version (show program's version number and exit) - - - # Examples - Allele mode: - - # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") - SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz - - K-mer mode: - - # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") - SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz - - # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") - SeqSero2_package.py -m k -t 4 -i assembly.fasta - - # Output - 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). - - - # Citation - Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. - SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. - **Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) - - 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) - -Keywords: Salmonella serotyping bioinformatics WGS -Platform: UNKNOWN -Classifier: Development Status :: 3 - Alpha -Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2) -Classifier: Programming Language :: Python :: 3 -Classifier: Topic :: Text Processing :: Linguistic diff -r 3e981acf8565 -r b1943f530c7b SeqSero2.egg-info/SOURCES.txt --- a/SeqSero2.egg-info/SOURCES.txt Mon Apr 27 01:31:22 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -LICENSE -MANIFEST.in -README.md -setup.py -version.py -SeqSero2.egg-info/PKG-INFO -SeqSero2.egg-info/SOURCES.txt -SeqSero2.egg-info/dependency_links.txt -SeqSero2.egg-info/not-zip-safe -SeqSero2.egg-info/requires.txt -SeqSero2.egg-info/top_level.txt -bin/Initial_Conditions.py -bin/SeqSero2_package.py -bin/SeqSero2_update_kmer_database.py -bin/deinterleave_fastq.sh -seqsero2_db/H_and_O_and_specific_genes.fasta -seqsero2_db/antigens.pickle -seqsero2_db/invA_mers_dict -seqsero2_db/special.pickle \ No newline at end of file diff -r 3e981acf8565 -r b1943f530c7b SeqSero2.egg-info/dependency_links.txt --- a/SeqSero2.egg-info/dependency_links.txt Mon Apr 27 01:31:22 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ - diff -r 3e981acf8565 -r b1943f530c7b SeqSero2.egg-info/not-zip-safe --- a/SeqSero2.egg-info/not-zip-safe Mon Apr 27 01:31:22 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ - diff -r 3e981acf8565 -r b1943f530c7b SeqSero2.egg-info/requires.txt --- a/SeqSero2.egg-info/requires.txt Mon Apr 27 01:31:22 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -biopython==1.73 diff -r 3e981acf8565 -r b1943f530c7b SeqSero2.egg-info/top_level.txt --- a/SeqSero2.egg-info/top_level.txt Mon Apr 27 01:31:22 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ - diff -r 3e981acf8565 -r b1943f530c7b dist/SeqSero2-1.1.0-py3.6.egg Binary file dist/SeqSero2-1.1.0-py3.6.egg has changed diff -r 3e981acf8565 -r b1943f530c7b dist/salmid-0.1.23-py3-none-any.whl Binary file dist/salmid-0.1.23-py3-none-any.whl has changed diff -r 3e981acf8565 -r b1943f530c7b dist/salmid-0.1.23.tar.gz Binary file dist/salmid-0.1.23.tar.gz has changed