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famseq
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public |
Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proceedings of the National Academy of Sciences. 2013 Mar 5;110(10):3985-90
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2024-12-11 |
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gemf_favites
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public |
User-friendly epidemic simulations
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2024-12-11 |
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radtk
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public |
A collection of tools for working with RAD files.
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2024-12-11 |
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fineradstructure
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public |
Inference of population structure from RAD datasets
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2024-12-11 |
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rnaz
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public |
predicting structural noncoding RNAs
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2024-12-11 |
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ucsc-genepredtobiggenepred
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public |
converts genePred or genePredExt to bigGenePred input (bed format with extra fields)
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2024-12-11 |
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pyrodigal
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public |
Python bindings to Prodigal, an ORF finder for microbial sequences.
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2024-12-11 |
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hardklor
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public |
Analyze mass spectra
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2024-12-11 |
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ucsc-checkcoveragegaps
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public |
Check for biggest gap in coverage for a list of tracks.
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2024-12-11 |
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debwt
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public |
A efficient method to construct BWT index of a given DNA sequence, especially
useful for gigantic and high similar genome.
DeBWT has good scalability to construct BWT in parallel computing.
It is well-suited to run on multiple core servers or clusters to
construct the BWT of large collections of genome sequences.
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2024-12-11 |
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verifybamid
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public |
No Summary
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2024-12-11 |
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ucsc-bamtopsl
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public |
Convert a bam file to a psl and optionally also a fasta file that contains the reads.
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2024-12-11 |
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mentalist
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public |
The MLST pipeline developed by the PathOGiST research group.
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2024-12-11 |
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comet-ms
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public |
Comet is a command line tool that does MS/MS database search.
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2024-12-11 |
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ucsc-hgloadbed
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public |
Load a generic bed file into database
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2024-12-11 |
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ucsc-mafcoverage
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public |
Analyse coverage by maf files - chromosome by
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2024-12-11 |
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ucsc-hgloadoutjoined
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public |
load new style (2014) RepeatMasker .out files into database
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2024-12-11 |
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mutscan
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public |
Detect and visualize target mutations by scanning FastQ files directly
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2024-12-11 |
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rainbow
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public |
Efficient tool for clustering and assembling short reads, especially for RAD
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2024-12-11 |
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rabbitqcplus
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public |
RabbitQCPlus is an efficient quality control tool for sequencing data
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2024-12-11 |
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ucsc-liftup
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public |
change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf
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2024-12-11 |
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treebest
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public |
TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline.
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2024-12-11 |
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irf
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public |
Inverted Repeats Finder is a program that detects approximate inverted repeats.
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2024-12-11 |
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gmtk
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public |
A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs)
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2024-12-11 |
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r-epic
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public |
Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
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2024-12-11 |
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ucsc-bedintersect
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public |
Intersect two bed files
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2024-12-11 |
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genesplicer
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public |
No Summary
|
2024-12-11 |
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ucsc-genepredsinglecover
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public |
create single-coverage genePred files
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2024-12-11 |
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ucsc-parasync
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public |
uses paraFetch to recursively mirror url to given path
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2024-12-11 |
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ncrf
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public |
Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data.
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2024-12-11 |
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tepeaks
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public |
Package for including repetitive regions in peak calling from ChIP-seq datasets.
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2024-12-11 |
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gnu-wget
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public |
No Summary
|
2024-12-11 |
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ucsc-validatefiles
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public |
Validates the format of different genomic files.
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2024-12-11 |
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strainseeker
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public |
A bacterial identification program for fast identification of bacterial strains from raw sequencing reads
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2024-12-11 |
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pcaone
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public |
PCAone - Principal Component Analysis All in One
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2024-12-11 |
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r-gwpcr
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public |
Implements the necessary distributions and parameter estimation procedures for a model of amplification and high-troughput sequencing. The model is based on a mechanistic model of PCR amplification as a Galton-Watson branching process, and on Poissonan sampling to model high-throughput sequencing.
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2024-12-11 |
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carpedeam
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public |
CarpeDeam - A metagenomic assembler for heavily damaged ancient datasets
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2024-12-11 |
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gefast
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public |
Clustering tool using Swarm's clustering strategy and Pass-Join's segment filter.
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2024-12-11 |
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msisensor
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public |
MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
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2024-12-11 |
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extract-sv-reads
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public |
Tool for extracting splitter or discordant reads from a BAM or CRAM file.
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2024-12-11 |
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plink
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public |
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
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2024-12-11 |
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flopp
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public |
flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing.
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2024-12-11 |
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ispcr
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public |
In silico PCR
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2024-12-11 |
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prophasm
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public |
ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs.
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2024-12-11 |
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kmerstream
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public |
Streaming algorithm for computing kmer statistics for massive genomics datasets
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2024-12-11 |
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extract_fullseq
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public |
extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
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2024-12-11 |
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ucsc-lavtopsl
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public |
Convert blastz lav to psl format
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2024-12-11 |
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filtlong
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public |
Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
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2024-12-11 |
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mgs-canopy
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public |
No Summary
|
2024-12-11 |
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ucsc-bigwigtobedgraph
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public |
Convert from bigWig to bedGraph format.
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2024-12-11 |
