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Name Modified Size Downloads / Week Status
Totals: 12 Items   92.4 MB 17
taxidfile.txt 2013-01-17 57.7 MB 11 weekly downloads
taxon_hierarchy.txt 2013-01-17 312.5 kB 22 weekly downloads
sample_usearch_results_97.txt 2013-01-17 28.0 MB 11 weekly downloads
sample_summary_rdp_97.txt 2013-01-17 727 Bytes 11 weekly downloads
sample_summary_strain_97..txt 2013-01-17 752 Bytes 11 weekly downloads
sample_summary_taxonomy_97.txt 2013-01-17 1.7 kB 33 weekly downloads
sample_assignment_97.txt 2013-01-17 828.2 kB 11 weekly downloads
sample_summary_97.txt 2013-01-17 543 Bytes 22 weekly downloads
vaginal_16S_V1V3_refdb1-1.fa 2013-01-17 666.2 kB 11 weekly downloads
sample.fasta 2013-01-17 4.9 MB 11 weekly downloads
stirrups_pipeline_1.0.pl 2013-01-17 16.9 kB 11 weekly downloads
stirrups_README.txt 2013-01-17 5.8 kB 22 weekly downloads
############################################# # STIRRUPS README ############################################# This document provides details on running the STIRRUPS script. ############################################# Requirements: 1.) STIRRUPS script 2.) Taxonomic ID File 3.) Taxonomic Hierarchy File 4.) Reference Library (Fasta Format) 5.) Sample Reads (Fasta Format) 6.) USEARCH version 4 or higher in path ############################################# Functionality: The STIRRUPS script takes a collection of reference fasta files and read fasta files and runs a USEARCH alignment. Using the resulting output from USEARCH it formats the output and calculates statistics based on percentage make up of a strain and species for a particular sample id. The script can optionally handle RDP data to perform additional analysis. If the USEARCH analysis is already run, USEARCH execution can be skipped so that only the results analysis is performed. ############################################# Usage: The program can be called in its most basic fashion using the following form: perl stirrups_pipeline.pl -l REFERENCE.fa -r READS.fa Example: perl stirrups_pipeline_1.0.pl -l vaginal_16S_V1V3_refdb1-1.fa -r sample.fasta In this example, vaginal_16S_V1V3_refdb1-1.fa is the FASTA formatted reference library and sample.fasta is the sample data to be processed. Note that example input files and the resulting output files (i.e., sample_summary_97.txt, sample_summary_rdp_97.txt, sample_summary_taxonomy_97.txt, sample_assignment_97.txt, and sample_usearch_results_97.txt) are provided. ############################################# Additional Options: The program supports a number of additional options for finer control: Options: -T VALUE Identity Threshold [default = 97] -nousearch Do not run USEARCH -rdp Fasta contains RDP data -strain Perform Strain Level Analysis Threshold: The threshold option controls the minimum identity score for reads to cluster together. No USEARCH: This option can be used if the USEARCH results are already avaialble and the alignment step is not necessary. The script will require the file to be named properly in order to execute. Example: INPUT FILE NAME: reads.fa USEARCH FILE NAME: reads_usearch_results_[threshold_value].txt To run the script without USEARCH, simply provide the base INPUT FILE NAME as normal, adding in the -nousearch option. The script will locate the approriate USEARCH FILE NAME for results analysis. RDP: The script can use RDP data to perform additional results analysis. If the input file contains RDP information, use the -rdp option. This will generate an additional rdp summary file and a taxonomic summary file. Strain: To generate an additional strain level analysis, enable this feature by using the -strain option. ############################################# Input Read File Format: This file should be a FASTA formatted file with each header containing a sample name followed by a read name. They should be separated by a "|". Examples:) >SAMPLE_NAME|READ_NAME >MOCK|HPD98O302INMJN If the file contains the optional RDP information, that should follow, again delimited by "|": Examples:) >SAMPLE_NAME|READ_NAME|RDP_TAXON|TAXON_LEVEL|RDP_CONFIDENCE_SCORE >MOCK|HPD98O302INMJN|Lactobacillaceae|family|0.84 RDP Confidence Scores range between 0.0 and 1.0 ############################################# Input Reference File Format: This file must also be FASTA formatted with headers that use the following format: Example:) >gi|173695|gb|M59083.1|genus|Acetitomaculum|species|ruminis|strain|Acetomaculum ruminis|start|31|end|509|length|479|details|AETRR16S/31-509 Acetomaculum ruminis 16S ribosomal RNA ############################################# Output Files: Assignment File: The assignment file describes which taxa a given read was assigned to. It will also provide the identity score of the given to that particular taxa. Summary File: The summary file describes the population of the various clusters. It gives the name of the sample, the name of the taxa, the number of reads in the taxa, the percentage of reads from the sample that mapped to that taxa, and the average identity score for the taxa. Taxonomy Summary File: The taxonomy file provides the full taxonomic breakdown for each taxa in addition to standard STIRRUPS results. RDP Summary File: The RDP summary file provides additional RDP catagorization information along with the standard STIRRUPS results. Strain Summary File: The strain summary file provides the standard STIRRUPS output with additional strain level detail for the taxa. USEARCH Results File: This file gives the raw output from the USEARCH program. ############################################# Citation: If you use the STIRRUPS method or software, or the 16S Vaginal Microbiome Database for your research, please cite: Fettweis JM, Serrano MG, Sheth NU, Mayer CM, Glascock AL, et al. (2012) Species-level classification of the vaginal microbiome. BMC Genomics 13: S17. doi:10.1186/1471-2164-13-S8-S17 Refer to the publication for additional information regarding the STIRRUPS method and appropriate usage. Note the the reference database file needs to be created or customized based on experimental design (e.g., select reference sequences to reflect body site or environment, trim reference sequences to primers, and cluster references into 'species-level taxa' based on sequencing orientation.) #############################################
Source: stirrups_README.txt, updated 2013-01-17

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