|
trimal
|
public |
A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
|
2024-12-13 |
|
miniprot
|
public |
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
|
2024-12-13 |
|
racon
|
public |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
|
2024-12-13 |
|
r-xmlrpc
|
public |
A simple implementation of XML-RPC for R.
|
2024-12-13 |
|
ucsc-pslswap
|
public |
Swap target and query in psls
|
2024-12-13 |
|
proda
|
public |
ProDA - Multiple alignment of protein sequences with repeated and shuffled elements
|
2024-12-13 |
|
ucsc-ratotab
|
public |
Convert ra file to table.
|
2024-12-13 |
|
ucsc-fetchchromsizes
|
public |
used to fetch chrom.sizes information from UCSC for the given <db>
|
2024-12-13 |
|
ucsc-nibsize
|
public |
print size of nibs
|
2024-12-13 |
|
mtsv-tools
|
public |
mtsv_tools contains core tools for alignment-based metagenomic binning
|
2024-12-13 |
|
hmmer
|
public |
Biosequence analysis using profile hidden Markov models
|
2024-12-13 |
|
peer
|
public |
A collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods
|
2024-12-13 |
|
mummer
|
public |
MUMmer is a system for rapidly aligning entire genomes
|
2024-12-13 |
|
amplici
|
public |
AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs.
|
2024-12-13 |
|
ucsc-hgfakeagp
|
public |
Create fake AGP file by looking at N's
|
2024-12-13 |
|
alcor
|
public |
Software for alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data.
|
2024-12-13 |
|
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 |
|
ucsc-positionaltblcheck
|
public |
check that positional tables are sorted
|
2024-12-13 |
|
unmerge
|
public |
Interlaced forward and reverse paired-end reads to individual forward and reverse files
|
2024-12-13 |
|
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 |
|
thesias
|
public |
Testing Haplotype Effects In Association Studies
|
2024-12-13 |
|
sickle-trim
|
public |
Windowed Adaptive Trimming for fastq files using quality
|
2024-12-13 |
|
maelstrom-core
|
public |
Rust utilities for NGS data processing.
|
2024-12-13 |
|
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 |
|
defiant
|
public |
Differential methylation, Easy, Fast, Identification and ANnoTation.
|
2024-12-13 |
|
relion
|
public |
Image-processing software for cryo-electron microscopy
|
2024-12-13 |
|
ucsc-chainsort
|
public |
Sort chains. By default sorts by score.
|
2024-12-13 |
|
ucsc-localtime
|
public |
convert unix timestamp to date string
|
2024-12-13 |
|
ucsc-rmfadups
|
public |
remove duplicate records in FA file
|
2024-12-13 |
|
satrap
|
public |
A SOLiD assembly translation program.
|
2024-12-13 |
|
ucsc-pslcat
|
public |
concatenate psl files
|
2024-12-13 |
|
bmtool
|
public |
bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-12-13 |
|
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 |
|
cyrcular
|
public |
Tool for calling circles from nanopore reads
|
2024-12-13 |
|
ac
|
public |
A lossless compression tool for Amino Acid sequences
|
2024-12-13 |
|
tssv
|
public |
Targeted characterisation of short structural variation.
|
2024-12-13 |
|
splitubam
|
public |
Split one ubam into multiple, per line, fast
|
2024-12-13 |
|
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 |
|
bwa-aln-interactive
|
public |
Version of the BWA aln read mapper for interactive alignment.
|
2024-12-13 |
|
assembly-stats
|
public |
Get assembly statistics from FASTA and FASTQ files
|
2024-12-13 |
|
bifrost
|
public |
Highly parallel construction and indexing of colored and compacted de Bruijn graphs
|
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 |
|
ucsc-chainswap
|
public |
Swap target and query in chain
|
2024-12-13 |
