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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.
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2024-12-13 |
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ucsc-fatofastq
|
public |
Convert fa to fastq format, just faking quality values.
|
2024-12-13 |
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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 |
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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
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2024-12-13 |
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bamutil
|
public |
Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
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2024-12-13 |
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velvet
|
public |
Sequence Assembler for short reads
|
2024-12-13 |
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qfilt
|
public |
No Summary
|
2024-12-13 |
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dsrc
|
public |
high-performance compression of sequencing reads stored in FASTQ format
|
2024-12-13 |
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ucsc-newprog
|
public |
make a new C source skeleton.
|
2024-12-13 |
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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 |
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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 |
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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 |
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phipack
|
public |
Simple, rapid, and statistically efficient test for recombination.
|
2024-12-13 |
|
ucsc-fasize
|
public |
print total base count in fa files.
|
2024-12-13 |
|
samblaster
|
public |
Mark duplicates in and extract discordant and split reads from SAM files.
|
2024-12-13 |
|
ucsc-axtswap
|
public |
Swap source and query in an axt file
|
2024-12-13 |
|
ucsc-randomlines
|
public |
Pick out random lines from file
|
2024-12-13 |
|
ucsc-pslhisto
|
public |
Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc.
|
2024-12-13 |
|
ucsc-ldhggene
|
public |
load database with gene predictions from a gff file.
|
2024-12-13 |
|
ucsc-pslcheck
|
public |
validate PSL files
|
2024-12-13 |
|
ucsc-fastqstatsandsubsample
|
public |
Go through a fastq file doing sanity checks and collecting stats
|
2024-12-13 |
|
pbmm2
|
public |
A minimap2 frontend for PacBio native data formats
|
2024-12-13 |
|
ucsc-ameme
|
public |
find common patterns in DNA
|
2024-12-13 |
|
lightassembler
|
public |
Lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other holding k-mers classified as likely correct, using a simple statistical test.
|
2024-12-13 |
|
ucsc-chainmergesort
|
public |
Combine sorted files into larger sorted file
|
2024-12-13 |
|
admixtools
|
public |
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
|
2024-12-13 |
|
ucsc-bigbedinfo
|
public |
Show information about a bigBed file.
|
2024-12-13 |
|
gocr
|
public |
GOCR is an OCR (Optical Character Recognition) program
|
2024-12-13 |
|
dnp-corrprofile
|
public |
Profile of correlations between the patterns of dinucleotide frequency on forward and reverse strands
|
2024-12-13 |
|
squizz
|
public |
Squizz is a sequence/alignment format checker, but it has some conversion capabilities too.
|
2024-12-13 |
|
harvesttools
|
public |
HarvestTools is a part of the Harvest software suite and provides file conversion between Gingr files and various standard text formats
|
2024-12-13 |
|
lz4-bin
|
public |
Extremely Fast Compression Application
|
2024-12-13 |
|
spades
|
public |
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
|
2024-12-13 |
|
macs2
|
public |
Model Based Analysis for ChIP-Seq data
|
2024-12-13 |
|
ucsc-bigbedsummary
|
public |
Extract summary information from a bigBed file.
|
2024-12-13 |
|
ucsc-pslscore
|
public |
calculate web blat score from psl files
|
2024-12-13 |
|
ncbi-ngs-sdk
|
public |
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
|
2024-12-13 |
|
abundancebin
|
public |
No Summary
|
2024-12-13 |
|
xtandem
|
public |
No Summary
|
2024-12-13 |
|
fasta3
|
public |
The FASTA package - protein and DNA sequence similarity searching and alignment programs
|
2024-12-13 |
|
minimap
|
public |
Experimental tool to find approximate mapping positions between long sequences
|
2024-12-13 |
|
libdivsufsort
|
public |
No Summary
|
2024-12-13 |
|
2pg_cartesian
|
public |
2pg cartesian is a framework of optimization algorithms for protein structure prediction.
|
2024-12-13 |
|
perl-data-uuid
|
public |
Globally/Universally Unique Identifiers (GUIDs/UUIDs)
|
2024-12-13 |
|
ucsc-paranodestart
|
public |
version 12.18
|
2024-12-13 |
|
karect
|
public |
Read error correction tool based on multiple alignment.
|
2024-12-13 |
|
allegro
|
public |
A fast linkage and haplotype analysis utility making use of MTBDD to reduce complexity.
|
2024-12-13 |
