Published October 27, 2021
| Version v1
Dataset
Open
BactPrep: A user-friendly whole-genome sequencing analysis platform for the detection of homologous recombination and horizontal gene transfer in bacteria - Sample Dataset
Description
This is the dataset used as the sample dataset for the pipeline BactPrep. This dataset consists of 218 Streptococcus pneumoniae PMEN1 WGS assemblies collected from the year 1984 - 2008 from 22 unique countries globally. The raw sequencing data was originally published in the work: Rapid pneumococcal evolution in response to clinical interventions (doi: 10.1371/journal.ppat.1002745) under the bioproject PRJEB2085.
We have assembled the raw sequences records with the following steps: 1) raw reads were first quality checked using fastQC 0.11.9; 2) adapters and low quality reads were removed using Trimmomatic 0.39 with parameter “ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”; 3) trimmed reads were error-corrected and assembled into WGS assemblies using SPAdes 3.15.0 with parameters "--careful --mismatch-correction”.
Files
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md5:a36cfe288f13920cc7cbc2277d6414c7
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2.1 MB | Download |
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md5:af0188d97961696964da597064924e70
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2.1 MB | Download |
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md5:a9e47eac07bdc831fb0101e7450f3407
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2.2 MB | Download |
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md5:58342cdc526e8adf07e657478fddf451
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2.1 MB | Download |
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md5:e2a765c2afc56c47bae8cebf222e1b77
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2.1 MB | Download |
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md5:c03333163f4e101ff4b3830647586182
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2.1 MB | Download |
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md5:b2fab38528160cd43c8f783e44163979
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2.1 MB | Download |
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md5:22d9cd170e23445f4fa4ed10fdb27a71
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2.1 MB | Download |
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md5:60afef99ee8b1e89beb085e8e3126ee1
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2.1 MB | Download |
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md5:2c09183f659fb760a3d59a3a5fc79b25
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2.1 MB | Download |
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md5:3fdd8bf5ae7d5c3520e60f4395731eef
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2.1 MB | Download |
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md5:7e54be22cae6fb5065014328a451f104
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2.1 MB | Download |
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md5:4b5921702176e7279e24121ccd3c38c0
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2.2 MB | Download |
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md5:3886f7380ad39b73678db48cb73c26ae
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2.2 MB | Download |
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md5:841ba8f32752a94a36b19e0117353a64
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2.2 MB | Download |
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md5:c21348735e0f01ae4fa72d94e88d64f5
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2.2 MB | Download |
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md5:9e754b901a525dceb11496d3f932bebb
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2.2 MB | Download |
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md5:53a359551210134ee32037fb9157c368
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2.2 MB | Download |