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seqprep
|
public |
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
|
2024-12-13 |
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ucsc-catuncomment
|
public |
Concatenate input removing lines that start with '#'
|
2024-12-13 |
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ucsc-paratestjob
|
public |
version 12.18
|
2024-12-13 |
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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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unmerge
|
public |
Interlaced forward and reverse paired-end reads to individual forward and reverse files
|
2024-12-13 |
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ucsc-blat
|
public |
Standalone BLAT v. 39x1 fast sequence search command line tool.
|
2024-12-13 |
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ucsc-maketablelist
|
public |
create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE)
|
2024-12-13 |
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fido
|
public |
No Summary
|
2024-12-13 |
|
thesias
|
public |
Testing Haplotype Effects In Association Studies
|
2024-12-13 |
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sickle-trim
|
public |
Windowed Adaptive Trimming for fastq files using quality
|
2024-12-13 |
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maelstrom-core
|
public |
Rust utilities for NGS data processing.
|
2024-12-13 |
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ucsc-twobittofa
|
public |
Convert all or part of .2bit file to fasta.
|
2024-12-13 |
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clustalo
|
public |
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
|
2024-12-13 |
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defiant
|
public |
Differential methylation, Easy, Fast, Identification and ANnoTation.
|
2024-12-13 |
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relion
|
public |
Image-processing software for cryo-electron microscopy
|
2024-12-13 |
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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 |
|
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 |
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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 |
|
qfilt
|
public |
No Summary
|
2024-12-13 |
|
foldcomp
|
public |
Foldcomp: a library and format for compressing and indexing large protein structure sets
|
2024-12-13 |
|
dsrc
|
public |
high-performance compression of sequencing reads stored in FASTQ format
|
2024-12-13 |
|
ucsc-newprog
|
public |
make a new C source skeleton.
|
2024-12-13 |
|
r-pophelper
|
public |
A set of useful functions for processing admixture proportion files from the population structure analysis softwares STRUCTURE, TESS, ADMIXTURE, BAPS, fastSTRUCTURE etc. The package contains functions to read runs, tabulate runs, summarise runs, plot runs, estimate K using Evanno method, export clumpp files, export distruct files and generate barplots.
|
2024-12-13 |
|
imseq
|
public |
IMSEQ is a fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobulin gene sequencing experiments
|
2024-12-13 |
|
snp-sites
|
public |
Finds SNP sites from a multi-FASTA alignment file.
|
2024-12-13 |
|
ideas
|
public |
A method for jointly and quantitatively characterizing multivariate epigenetic landscapes in many cell types, tissues or conditions.
|
2024-12-13 |
|
nseg
|
public |
nseg identifies and masks regions of low complexity in nucleic acid sequences
|
2024-12-13 |
|
phipack
|
public |
Simple, rapid, and statistically efficient test for recombination.
|
2024-12-13 |
|
longshot
|
public |
Diploid SNV caller for error-prone reads.
|
2024-12-13 |
|
ucsc-fasize
|
public |
print total base count in fa files.
|
2024-12-13 |
|
yak
|
public |
Yet another k-mer analyzer
|
2024-12-13 |
|
samblaster
|
public |
Mark duplicates in and extract discordant and split reads from SAM files.
|
2024-12-13 |
