SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION

PRINSEQ 0.20.4 – Preprocess and Generate Statistics about Sequence data

PRINSEQ 0.20.4

:: DESCRIPTION

PRINSEQ (PReprocessing and INformation of SEQuence data.) is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a user-friendly web interface or as standalone version. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.

PRINSEQ Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 PRINSEQ

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Quality control and preprocessing of metagenomic datasets.
Bioinformatics 2011, 27:863-864.

MetaCon – Unsupervised Clustering of Metagenomic Contigs with Probabilistic k-mers Statistics and Coverage

MetaCon

:: DESCRIPTION

MetaCon is a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MetaCon

:: MORE INFORMATION

Citation

BMC Bioinformatics, 20 (Suppl 9), 367 2019 Nov 22
MetaCon: Unsupervised Clustering of Metagenomic Contigs With Probabilistic K-Mers Statistics and Coverage
Jia Qian, Matteo Comin

PC-select – Calculation of GWAS Association Statistics

PC-select

:: DESCRIPTION

PC-select calculates GWAS association statistics using a data-adaptive GRM that improves power over standard mixed models while simultaneously avoiding confounding from population stratification.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PC-select

:: MORE INFORMATION

Citation:

Genetics. 2014 Jul;197(3):1045-9. doi: 10.1534/genetics.114.164285. Epub 2014 Apr 29.
Improving the power of GWAS and avoiding confounding from population stratification with PC-Select.
Tucker G, Price AL, Berger B

DIST 1.0.0 / DISTMIX v0.2.0- Direct Imputation of summary STatistics for unmeasured SNPs /from mixed Ethnicity Cohorts

DIST 1.0.0 / DISTMIX v0.2.0

:: DESCRIPTION

DIST is a software program for directly imputing the normally distributed summary statistics of unmeasured SNPs in a GWAS/meta-analysis without first imputing subject level genotypes.

DISTMIX is a very fast and novel software program for Directly Imputing summary STatistics (two-tailed Z-scores) for unmeasured SNPs from MIXed ethnicity cohorts using measured SNP summary data (including cohort allele frequencies) from the cohorts and external reference populations such as 1000 Genomes data.

::DEVELOPER

DIST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DIST / DISTMIX

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 15;29(22):2925-7. doi: 10.1093/bioinformatics/btt500. Epub 2013 Aug 28.
DIST: direct imputation of summary statistics for unmeasured SNPs.
Lee D1, Bigdeli TB, Riley BP, Fanous AH, Bacanu SA.

DISTMIX: Direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts.
Lee D, Bigdeli TB, Williamson VS, Vladimirov VI, Riley BP, Fanous AH, Bacanu SA.
Bioinformatics. 2015 Jun 9. pii: btv348.

Pedgene 2.1 – Gene-level Statistics for Pedigree Data

Pedgene 2.1

:: DESCRIPTION

Pedgene offers an R package that performs gene-level kernel and burden association tests for genetic variants with disease status and continuous traits for pedigree data and unrelated subjects.

::DEVELOPER

Statistical Genetics and Genetic Epidemiology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 Pedgene

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Jul;37(5):409-18. doi: 10.1002/gepi.21727. Epub 2013 May 5.
Multiple genetic variant association testing by collapsing and kernel methods with pedigree or population structured data.
Schaid DJ1, McDonnell SK, Sinnwell JP, Thibodeau SN.

KmerStream 1.0 – Computing kmer statistics for massive Genomics Datasets

KmerStream 1.0

:: DESCRIPTION

KmerStream is a streaming algorithm for estimating the number of distinct k-mers present in high throughput sequencing data.

::DEVELOPER

Pall Melsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • C++ COmpiler

:: DOWNLOAD

 KmerStream

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 28. pii: btu713.
KmerStream: Streaming algorithms for k-mer abundance estimation.
Melsted P, Halldórsson BV

P.R.E.S.S. 2.0 – Exploring Residual-level Protein Structural Statistics

P.R.E.S.S. 2.0

:: DESCRIPTION

P.R.E.S.S. (Protein Residue-Level Structural Statistics) is an R-package developed to allow researchers to get access to and manipulate on a large set of statistical data on protein residue-level structural properties such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles.

::DEVELOPER

PRESS Team

:: SCREENSHOTS

press

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 P.R.E.S.S.

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2012 Jun;10(3):1242007. doi: 10.1142/S0219720012420073.
P.R.E.S.S.–an R-package for exploring residual-level protein structural statistics.
Huang Y, Bonett S, Kloczkowski A, Jernigan R, Wu Z.