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sparc
|
public |
No Summary
|
2024-12-13 |
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verse
|
public |
VERSE: a versatile and efficient RNA-Seq read counting tool
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2024-12-13 |
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lordfast
|
public |
Sensitive and Fast Alignment Search Tool for Long Read sequencing Data
|
2024-12-13 |
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ucsc-tolower
|
public |
Convert upper case to lower case in file. Leave other chars alone
|
2024-12-13 |
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anise_basil
|
public |
BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. ANISE is a method for the assembly of large insertions from paired reads in BAM format and a list candidate insert breakpoints as generated by BASIL.
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2024-12-13 |
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mapdia
|
public |
Performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs.
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2024-12-13 |
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red
|
public |
Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
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2024-12-13 |
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hapbin
|
public |
hapbin is a collection of tools for efficiently calculating Extended Haplotype Homozygosity (EHH), the Integrated Haplotype Score (iHS) and the Cross Population Extended Haplotype Homozogysity (XP-EHH) statistic.
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2024-12-13 |
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ucsc-addcols
|
public |
Sum columns in a text file.
|
2024-12-13 |
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ucsc-avecols
|
public |
average together columns
|
2024-12-13 |
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ucsc-chainsplit
|
public |
Split chains up by target or query sequence
|
2024-12-13 |
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ucsc-fapolyasizes
|
public |
get poly A sizes
|
2024-12-13 |
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rust-ncbitaxonomy
|
public |
A Rust crate for working with a local copy of the NCBI Taxonomy database, which provides utilities for taxonomic filtering.
|
2024-12-13 |
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ucsc-hgbbidblink
|
public |
Add table that just contains a pointer to a bbiFile to database. This program
|
2024-12-13 |
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ucsc-mktime
|
public |
convert date string to unix timestamp
|
2024-12-13 |
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trimal
|
public |
A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
|
2024-12-13 |
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racon
|
public |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
|
2024-12-13 |
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r-xmlrpc
|
public |
A simple implementation of XML-RPC for R.
|
2024-12-13 |
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ucsc-pslswap
|
public |
Swap target and query in psls
|
2024-12-13 |
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ucsc-ratotab
|
public |
Convert ra file to table.
|
2024-12-13 |
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ucsc-fetchchromsizes
|
public |
used to fetch chrom.sizes information from UCSC for the given <db>
|
2024-12-13 |
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ucsc-nibsize
|
public |
print size of nibs
|
2024-12-13 |
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hmmer
|
public |
Biosequence analysis using profile hidden Markov models
|
2024-12-13 |
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mummer
|
public |
MUMmer is a system for rapidly aligning entire genomes
|
2024-12-13 |
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ucsc-hgfakeagp
|
public |
Create fake AGP file by looking at N's
|
2024-12-13 |
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seqprep
|
public |
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
|
2024-12-13 |
|
ucsc-catuncomment
|
public |
Concatenate input removing lines that start with '#'
|
2024-12-13 |
|
ucsc-paratestjob
|
public |
version 12.18
|
2024-12-13 |
|
ucsc-bigbedtobed
|
public |
Convert from bigBed to ascii bed format.
|
2024-12-13 |
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ucsc-positionaltblcheck
|
public |
check that positional tables are sorted
|
2024-12-13 |
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ucsc-blat
|
public |
Standalone BLAT v. 39x1 fast sequence search command line tool.
|
2024-12-13 |
|
ucsc-maketablelist
|
public |
create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE)
|
2024-12-13 |
|
fido
|
public |
No Summary
|
2024-12-13 |
|
sickle-trim
|
public |
Windowed Adaptive Trimming for fastq files using quality
|
2024-12-13 |
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ucsc-twobittofa
|
public |
Convert all or part of .2bit file to fasta.
|
2024-12-13 |
|
clustalo
|
public |
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
|
2024-12-13 |
|
ucsc-chainsort
|
public |
Sort chains. By default sorts by score.
|
2024-12-13 |
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ucsc-localtime
|
public |
convert unix timestamp to date string
|
2024-12-13 |
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ucsc-rmfadups
|
public |
remove duplicate records in FA file
|
2024-12-13 |
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satrap
|
public |
A SOLiD assembly translation program.
|
2024-12-13 |
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ucsc-pslcat
|
public |
concatenate psl files
|
2024-12-13 |
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bmtool
|
public |
bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-12-13 |
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rscape
|
public |
R-scape (RNA Structural Covariation Above Phylogenetic Expectation) looks for evidence of a conserved RNA secondary structure by measuring pairwise covariations observed in an input multiple sequence alignment.
|
2024-12-13 |
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ucsc-fatofastq
|
public |
Convert fa to fastq format, just faking quality values.
|
2024-12-13 |
|
mreps
|
public |
mreps is a flexible and efficient software for identifying serial repeats (usually called tandem repeats) in DNA sequences.
|
2024-12-13 |
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assembly-stats
|
public |
Get assembly statistics from FASTA and FASTQ files
|
2024-12-13 |
|
bloomfiltertrie
|
public |
An alignment-free, reference-free and incremental data structure for colored de Bruijn graph with application to pan-genome indexing.
|
2024-12-13 |
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ucsc-chainswap
|
public |
Swap target and query in chain
|
2024-12-13 |
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bamutil
|
public |
Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
|
2024-12-13 |
|
velvet
|
public |
Sequence Assembler for short reads
|
2024-12-13 |
