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ucsc-bamtopsl
|
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 |
|
mentalist
|
public |
The MLST pipeline developed by the PathOGiST research group.
|
2024-12-11 |
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mbuffer
|
public |
mbuffer is a tool for buffering data streams with a large set of unique features
|
2024-12-11 |
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comet-ms
|
public |
Comet is a command line tool that does MS/MS database search.
|
2024-12-11 |
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ucsc-hgloadbed
|
public |
Load a generic bed file into database
|
2024-12-11 |
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ucsc-mafcoverage
|
public |
Analyse coverage by maf files - chromosome by
|
2024-12-11 |
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ucsc-hgloadoutjoined
|
public |
load new style (2014) RepeatMasker .out files into database
|
2024-12-11 |
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mutscan
|
public |
Detect and visualize target mutations by scanning FastQ files directly
|
2024-12-11 |
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rainbow
|
public |
Efficient tool for clustering and assembling short reads, especially for RAD
|
2024-12-11 |
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rabbitqcplus
|
public |
RabbitQCPlus is an efficient quality control tool for sequencing data
|
2024-12-11 |
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ucsc-liftup
|
public |
change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf
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2024-12-11 |
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treebest
|
public |
TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline.
|
2024-12-11 |
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irf
|
public |
Inverted Repeats Finder is a program that detects approximate inverted repeats.
|
2024-12-11 |
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gmtk
|
public |
A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs)
|
2024-12-11 |
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r-epic
|
public |
Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
|
2024-12-11 |
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ucsc-bedintersect
|
public |
Intersect two bed files
|
2024-12-11 |
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genesplicer
|
public |
No Summary
|
2024-12-11 |
|
ucsc-genepredsinglecover
|
public |
create single-coverage genePred files
|
2024-12-11 |
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ucsc-parasync
|
public |
uses paraFetch to recursively mirror url to given path
|
2024-12-11 |
|
ncrf
|
public |
Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data.
|
2024-12-11 |
|
tepeaks
|
public |
Package for including repetitive regions in peak calling from ChIP-seq datasets.
|
2024-12-11 |
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gnu-wget
|
public |
No Summary
|
2024-12-11 |
|
ucsc-validatefiles
|
public |
Validates the format of different genomic files.
|
2024-12-11 |
|
strainseeker
|
public |
A bacterial identification program for fast identification of bacterial strains from raw sequencing reads
|
2024-12-11 |
|
pcaone
|
public |
PCAone - Principal Component Analysis All in One
|
2024-12-11 |
|
r-gwpcr
|
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.
|
2024-12-11 |
|
carpedeam
|
public |
CarpeDeam - A metagenomic assembler for heavily damaged ancient datasets
|
2024-12-11 |
|
gefast
|
public |
Clustering tool using Swarm's clustering strategy and Pass-Join's segment filter.
|
2024-12-11 |
|
msisensor
|
public |
MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
|
2024-12-11 |
|
extract-sv-reads
|
public |
Tool for extracting splitter or discordant reads from a BAM or CRAM file.
|
2024-12-11 |
|
galaxy-schema
|
public |
The Galaxy API schema objects.
|
2024-12-11 |
|
galaxy-data
|
public |
The Galaxy models, datatype framework, and datatype implementations.
|
2024-12-11 |
|
galaxy-files
|
public |
The Galaxy file sources framework and default plugins.
|
2024-12-11 |
|
galaxy-objectstore
|
public |
The Galaxy object store framework and default implementations
|
2024-12-11 |
|
plink
|
public |
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
|
2024-12-11 |
|
flopp
|
public |
flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing.
|
2024-12-11 |
|
ispcr
|
public |
In silico PCR
|
2024-12-11 |
|
prophasm
|
public |
ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs.
|
2024-12-11 |
|
kmerstream
|
public |
Streaming algorithm for computing kmer statistics for massive genomics datasets
|
2024-12-11 |
|
extract_fullseq
|
public |
extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-12-11 |
|
ucsc-lavtopsl
|
public |
Convert blastz lav to psl format
|
2024-12-11 |
|
filtlong
|
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.
|
2024-12-11 |
|
mgs-canopy
|
public |
No Summary
|
2024-12-11 |
|
ucsc-bigwigtobedgraph
|
public |
Convert from bigWig to bedGraph format.
|
2024-12-11 |
|
htsbox
|
public |
HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files.
|
2024-12-11 |
|
ir
|
public |
Program for Calculating the Repetitiveness of DNA Sequences
|
2024-12-11 |
|
ucsc-pslliftsubrangeblat
|
public |
lift PSLs from blat subrange alignments
|
2024-12-11 |
|
ococo
|
public |
Ococo, the first online consensus caller.
|
2024-12-11 |
|
potrace
|
public |
A tool for tracing a bitmap, which means, transforming a bitmap into a smooth, scalable image
|
2024-12-11 |
|
seqyclean
|
public |
Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
|
2024-12-11 |
