Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

Therkildsen NO, Palumbi SR

Date Published: August 3, 2016

DOI: http://dx.doi.org/10.5061/dryad.ft596

 

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Title Commands for running the pipeline
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Description This file contains a list of the programs and parameter values we used for the bioinformatic analysis pipeline described in the paper. Note that the sequence of steps described in this file was designed to carefully evaluate the quality of sequencing data generated with a new library preparation method. For routine applications (where it may not be necessary to quantify the loss of data at each individual filtering step), several steps can be skipped, optimized or combined for a more streamlined pipeline.
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Title QC_Stats_Therkildsen_and_Palumbi
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Description This Excel file contains the raw data used to evaluate the quality of sequencing libraries. Please see the tab "Column title descriptions" for explanations of the column headers.
Download QC_Stats_Therkildsen_and_Palumbi.xlsx (1.098 Mb)
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Title RemoveSequencesFromFastq.py
Downloaded 8 times
Description A simple python script for removing specific sequences (named in an input file) from a fastq file. Our pipeline uses this script to removing potential contaminant reads prior to mapping to the reference.
Download RemoveSequencesFromFastq.py (1.122 Kb)
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When using this data, please cite the original publication:

Therkildsen NO, Palumbi SR (2017) Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Molecular Ecology Resources 17(2): 194–208. http://dx.doi.org/10.1111/1755-0998.12593

Additionally, please cite the Dryad data package:

Therkildsen NO, Palumbi SR (2016) Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ft596
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