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cyrcular
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public |
Tool for calling circles from nanopore reads
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2024-12-13 |
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ac
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public |
A lossless compression tool for Amino Acid sequences
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2024-12-13 |
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tssv
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public |
Targeted characterisation of short structural variation.
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2024-12-13 |
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splitubam
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public |
Split one ubam into multiple, per line, fast
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2024-12-13 |
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ucsc-fatofastq
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public |
Convert fa to fastq format, just faking quality values.
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2024-12-13 |
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mreps
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public |
mreps is a flexible and efficient software for identifying serial repeats (usually called tandem repeats) in DNA sequences.
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2024-12-13 |
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bwa-aln-interactive
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public |
Version of the BWA aln read mapper for interactive alignment.
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2024-12-13 |
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assembly-stats
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public |
Get assembly statistics from FASTA and FASTQ files
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2024-12-13 |
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bifrost
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public |
Highly parallel construction and indexing of colored and compacted de Bruijn graphs
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2024-12-13 |
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bloomfiltertrie
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public |
An alignment-free, reference-free and incremental data structure for colored de Bruijn graph with application to pan-genome indexing.
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2024-12-13 |
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ucsc-chainswap
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public |
Swap target and query in chain
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2024-12-13 |
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bamutil
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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
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2024-12-13 |
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qfilt
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public |
No Summary
|
2024-12-13 |
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foldcomp
|
public |
Foldcomp: a library and format for compressing and indexing large protein structure sets
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2024-12-13 |
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dsrc
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public |
high-performance compression of sequencing reads stored in FASTQ format
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2024-12-13 |
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ucsc-newprog
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public |
make a new C source skeleton.
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2024-12-13 |
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r-pophelper
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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.
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2024-12-13 |
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imseq
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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
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2024-12-13 |
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snp-sites
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public |
Finds SNP sites from a multi-FASTA alignment file.
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2024-12-13 |
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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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nseg
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public |
nseg identifies and masks regions of low complexity in nucleic acid sequences
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2024-12-13 |
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phipack
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public |
Simple, rapid, and statistically efficient test for recombination.
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2024-12-13 |
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longshot
|
public |
Diploid SNV caller for error-prone reads.
|
2024-12-13 |
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ucsc-fasize
|
public |
print total base count in fa files.
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2024-12-13 |
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yak
|
public |
Yet another k-mer analyzer
|
2024-12-13 |
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samblaster
|
public |
Mark duplicates in and extract discordant and split reads from SAM files.
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2024-12-13 |
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sam2pairwise
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public |
sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read
|
2024-12-13 |
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ucsc-axtswap
|
public |
Swap source and query in an axt file
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2024-12-13 |
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ucsc-randomlines
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public |
Pick out random lines from file
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2024-12-13 |
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ucsc-pslhisto
|
public |
Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc.
|
2024-12-13 |
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ucsc-ldhggene
|
public |
load database with gene predictions from a gff file.
|
2024-12-13 |
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ucsc-pslcheck
|
public |
validate PSL files
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2024-12-13 |
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ucsc-fastqstatsandsubsample
|
public |
Go through a fastq file doing sanity checks and collecting stats
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2024-12-13 |
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popins2
|
public |
Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
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2024-12-13 |
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saccharis
|
public |
A CAZyme discovery tool. Easily create phylogenetic trees from FASTA files and CAZyme families.
|
2024-12-13 |
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pbmm2
|
public |
A minimap2 frontend for PacBio native data formats
|
2024-12-13 |
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deepfplearn
|
public |
Link molecular structures of chemicals (in form of topological fingerprints) with multiple targets.
|
2024-12-13 |
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konezumiaid
|
public |
This is used for automatically designing gRNAs for genome editing by Target-AID.
|
2024-12-13 |
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kmertools
|
public |
kmertools: DNA Vectorisation Tool
|
2024-12-13 |
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nanoplexer
|
public |
Tool for demultiplexing Nanopore barcode sequence data
|
2024-12-13 |
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ucsc-ameme
|
public |
find common patterns in DNA
|
2024-12-13 |
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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 |
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ucsc-chainmergesort
|
public |
Combine sorted files into larger sorted file
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2024-12-13 |
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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 |
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ucsc-bigbedinfo
|
public |
Show information about a bigBed file.
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2024-12-13 |
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iow
|
public |
Implementation of Balanced Parentheses
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2024-12-13 |
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ibdmix
|
public |
ibdmix: estimate introgression by IBD
|
2024-12-13 |
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sankoff
|
public |
Fast implementation of sankoff algorithm on phylogeny
|
2024-12-13 |
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gocr
|
public |
GOCR is an OCR (Optical Character Recognition) program
|
2024-12-13 |
