Data from: Whole genome amplification and reduced-representation genome sequencing of Schistosoma japonicum miracidia

Shortt JA, Card DC, Schield DR, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD

Date Published: January 24, 2017

DOI: http://dx.doi.org/10.5061/dryad.8091q

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title adult_worm_and_eight_miracidia_stringent_filter
Downloaded 15 times
Description vcf comprised of stringently filtered variants found from ddRADseq in S. japonicum adult worm and eight miracidia samples.
Download all_samples.vcf (13.59 Mb)
Details View File Details
Title mircidia_only_stringent_filter
Downloaded 12 times
Description vcf comprised of stringently filtered variants found from ddRADseq in 8 S. japonicum miracidia samples.
Download all_miracidia.vcf (31.96 Mb)
Details View File Details
Title miracidia_missing25_stringent_filter
Downloaded 14 times
Description vcf comprised of variants found in ddRADseq in at least 75% of eight S. japonicum miracidia.
Download miracidia_missing25.vcf (50.55 Mb)
Details View File Details
Title miracidia_only_loose_filter
Downloaded 16 times
Description vcf comprised of loosely filtered variants from ddRADseq of eight S japonicum miracidia
Download miracidia_all_samples_filtered_variable.vcf (32.81 Mb)
Details View File Details
Title haplotype_caller_unfiltered
Downloaded 6 times
Description unfiltered vcf from S. japonucum adult worm and 8 miracidia generated using GATK haplotype caller
Download output.all.test1.gvcf (74.49 Mb)
Details View File Details
Title unified_genotyper_all_samples_unfiltered
Downloaded 17 times
Description unfiltered vcf from S. japonucum adult worm and 8 miracidia generated using GATK unified genotyper.
Download schisto_align.merged.bam.realigned.bam.fi...ts.vcf (532.6 Mb)
Details View File Details
Title multi_cov_by_len
Downloaded 7 times
Description # Used to determine coverage of features in a bed file using the alignments in a bam file. # Output lists the length of features, number of features of that length, and percentage of features of that length recovered in the bam file. # Script reads in output from bedtools coverage command executed as follows: bedtools coverage -hist -abam [bam_infile] -b [bed_file] > [output]
Download multi_cov_by_len.pl (2.798 Kb)
Details View File Details
Title proportion_het_v2
Downloaded 9 times
Description Returns the proportion of heterozygous variants for each sample in a .vcf
Download proportion_het_v2.pl (3.633 Kb)
Details View File Details
Title var_sharing_sampling
Downloaded 9 times
Description calculates pairwise similarity of genotypes between samples of a vcf
Download var_sharing_sampling.pl (5.852 Kb)
Details View File Details
Title check_radtag_from_sam
Downloaded 9 times
Description counts the number of times a provided restriction site sequence is found at the beginning of a sequence read from a .sam file
Download check_radtag_from_sam.pl (2.869 Kb)
Details View File Details
Title cutgenome.v0.04
Downloaded 6 times
Description Returns .bed file with double digested fragments from a provided genome and cut sites
Download cutgenome.v0.04.pl (3.052 Kb)
Details View File Details
Title S4Table_microsatellite_primers
Downloaded 5 times
Download S4Table.xlsx (230.3 Kb)
Details View File Details
Title vcffilter.py
Downloaded 9 times
Description Filters vcf. Removes monomorphic or non-bi-allelic variants, and codes individual genotypes as missing data if the genotype quality score is below 20 or individual read depth is below 10.
Download vcffilter (3.804 Kb)
Details View File Details

When using this data, please cite the original publication:

Shortt JA, Card DC, Schield DR, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD (2017) Whole genome amplification and reduced-representation genome sequencing of Schistosoma japonicum miracidia. PLOS Neglected Tropical Diseases 11(1): e0005292. http://dx.doi.org/10.1371/journal.pntd.0005292

Additionally, please cite the Dryad data package:

Shortt JA, Card DC, Schield DR, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD (2017) Data from: Whole genome amplification and reduced-representation genome sequencing of Schistosoma japonicum miracidia. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8091q
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: