flash2
|
public |
Merge paired-end reads from fragments that are shorter than twice the read length
|
2024-12-11 |
plass
|
public |
Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide assembler) are methods to assemble short read sequencing data on a protein level to proteins or DNA contigs
|
2024-12-11 |
perl-config-any
|
public |
Load configuration from different file formats, transparently
|
2024-12-11 |
mdasim
|
public |
This is MDAsim 2+, a tool to simulate whole genome amplification of a DNA sequence with multiple displacement amplification. A citation for this version will be provided when available. MDAsim 2+ extends MDAsim 1.2, so please also always cite: Tagliavi Z, Draghici S. MDAsim: A multiple displacement amplification simulator. 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2012. pp. 1–4. doi:10.1109/BIBM.2012.6392622
|
2024-12-11 |
ucsc-hubpubliccheck
|
public |
checks that the labels in hubPublic match what is in the hub labels
|
2024-12-11 |
sparseassembler
|
public |
No Summary
|
2024-12-11 |
ucsc-gtftogenepred
|
public |
convert a GTF file to a genePred
|
2024-12-11 |
mageck
|
public |
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.
|
2024-12-11 |
perl-tie-hash-indexed
|
public |
Ordered hashes for Perl
|
2024-12-11 |
mummer4
|
public |
MUMmer is a system for rapidly aligning entire genomes
|
2024-12-11 |
r2r
|
public |
software to speed depiction of aesthetic consensus RNA secondary structures
|
2024-12-11 |
heinz
|
public |
The algorithm for identification of the optimal scoring subnetwork.
|
2024-12-11 |
perl-filesys-df
|
public |
Perl extension for filesystem disk space information.
|
2024-12-11 |
famseq
|
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
|
2024-12-11 |
rnaz
|
public |
predicting structural noncoding RNAs
|
2024-12-11 |
ucsc-genepredtobiggenepred
|
public |
converts genePred or genePredExt to bigGenePred input (bed format with extra fields)
|
2024-12-11 |
hardklor
|
public |
Analyze mass spectra
|
2024-12-11 |
ucsc-checkcoveragegaps
|
public |
Check for biggest gap in coverage for a list of tracks.
|
2024-12-11 |
debwt
|
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.
|
2024-12-11 |
verifybamid
|
public |
No Summary
|
2024-12-11 |
ucsc-bamtopsl
|
public |
Convert a bam file to a psl and optionally also a fasta file that contains the reads.
|
2024-12-11 |
mentalist
|
public |
The MLST pipeline developed by the PathOGiST research group.
|
2024-12-11 |
mbuffer
|
public |
mbuffer is a tool for buffering data streams with a large set of unique features
|
2024-12-11 |
comet-ms
|
public |
Comet is a command line tool that does MS/MS database search.
|
2024-12-11 |
ucsc-hgloadbed
|
public |
Load a generic bed file into database
|
2024-12-11 |
ucsc-mafcoverage
|
public |
Analyse coverage by maf files - chromosome by
|
2024-12-11 |
ucsc-hgloadoutjoined
|
public |
load new style (2014) RepeatMasker .out files into database
|
2024-12-11 |
rainbow
|
public |
Efficient tool for clustering and assembling short reads, especially for RAD
|
2024-12-11 |
ucsc-liftup
|
public |
change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf
|
2024-12-11 |
treebest
|
public |
TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline.
|
2024-12-11 |
gmtk
|
public |
A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs)
|
2024-12-11 |
r-epic
|
public |
Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
|
2024-12-11 |
ucsc-bedintersect
|
public |
Intersect two bed files
|
2024-12-11 |
genesplicer
|
public |
No Summary
|
2024-12-11 |
ucsc-genepredsinglecover
|
public |
create single-coverage genePred files
|
2024-12-11 |
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 |
gnu-wget
|
public |
No Summary
|
2024-12-11 |
ucsc-validatefiles
|
public |
Validates the format of different genomic files.
|
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 |
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 |
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 |
prophasm
|
public |
ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs.
|
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 |