Mercurial > repos > cstrittmatter > ss2v110

--- a/SeqSero2.egg-info/PKG-INFO	Mon Apr 27 01:31:22 2020 -0400
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-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 <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a)
-
-            -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)
-
-            -i <file> (/path/to/input/file)
-
-            -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)
-
-            -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)
-
-            -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number)
-
-            -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files)
-
-            -n <string> (optional, to specify a sample name in the report output)
-
-            -s <flag> (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv)
-
-            --check <flag> (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
--- a/SeqSero2.egg-info/SOURCES.txt	Mon Apr 27 01:31:22 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-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
--- a/SeqSero2.egg-info/dependency_links.txt	Mon Apr 27 01:31:22 2020 -0400
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-
--- 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
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-
--- 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
--- a/SeqSero2.egg-info/top_level.txt	Mon Apr 27 01:31:22 2020 -0400
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-
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