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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
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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
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2024-12-13 |
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foldcomp
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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
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public |
A method for jointly and quantitatively characterizing multivariate epigenetic landscapes in many cell types, tissues or conditions.
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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
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public |
Diploid SNV caller for error-prone reads.
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2024-12-13 |
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ucsc-fasize
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public |
print total base count in fa files.
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2024-12-13 |
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yak
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public |
Yet another k-mer analyzer
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2024-12-13 |
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samblaster
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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
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2024-12-13 |
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ucsc-axtswap
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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
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public |
Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc.
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2024-12-13 |
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ucsc-ldhggene
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public |
load database with gene predictions from a gff file.
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2024-12-13 |
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ucsc-pslcheck
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public |
validate PSL files
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2024-12-13 |
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ucsc-fastqstatsandsubsample
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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
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public |
A CAZyme discovery tool. Easily create phylogenetic trees from FASTA files and CAZyme families.
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2024-12-13 |
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pbmm2
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public |
A minimap2 frontend for PacBio native data formats
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2024-12-13 |
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deepfplearn
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public |
Link molecular structures of chemicals (in form of topological fingerprints) with multiple targets.
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2024-12-13 |
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konezumiaid
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public |
This is used for automatically designing gRNAs for genome editing by Target-AID.
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2024-12-13 |
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kmertools
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public |
kmertools: DNA Vectorisation Tool
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2024-12-13 |
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nanoplexer
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public |
Tool for demultiplexing Nanopore barcode sequence data
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2024-12-13 |
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ucsc-ameme
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public |
find common patterns in DNA
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2024-12-13 |
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lightassembler
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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.
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2024-12-13 |
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ucsc-chainmergesort
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public |
Combine sorted files into larger sorted file
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2024-12-13 |
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admixtools
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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.
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2024-12-13 |
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ucsc-bigbedinfo
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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
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2024-12-13 |
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sankoff
|
public |
Fast implementation of sankoff algorithm on phylogeny
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2024-12-13 |
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gocr
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public |
GOCR is an OCR (Optical Character Recognition) program
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2024-12-13 |
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dnp-corrprofile
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public |
Profile of correlations between the patterns of dinucleotide frequency on forward and reverse strands
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2024-12-13 |
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maf2synteny
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public |
A tool that postprocesses whole genome alignment (for two or more genomes) and produces coarse-grained synteny blocks.
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2024-12-13 |
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kalign3
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public |
Kalign is a fast and accurate multiple sequence alignment algorithm.
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2024-12-13 |
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squizz
|
public |
Squizz is a sequence/alignment format checker, but it has some conversion capabilities too.
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2024-12-13 |
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hilive2
|
public |
Tool for real-time read alignment of Illumina sequencing data
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2024-12-13 |
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harvesttools
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public |
HarvestTools is a part of the Harvest software suite and provides file conversion between Gingr files and various standard text formats
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2024-12-13 |
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lca
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public |
LCA - Lowest Common Ancestor calculation tool
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2024-12-13 |
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cagee
|
public |
Analyzes changes in gene expression in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences
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2024-12-13 |
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lz4-bin
|
public |
Extremely Fast Compression Application
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2024-12-13 |
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polypolish
|
public |
Polishing genome assemblies with short reads.
|
2024-12-13 |
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spades
|
public |
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
|
2024-12-13 |
