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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
|
public |
Swap source and query in an axt file
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2024-12-13 |
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ucsc-randomlines
|
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.
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2024-12-13 |
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ucsc-ldhggene
|
public |
load database with gene predictions from a gff file.
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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.
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2024-12-13 |
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pbmm2
|
public |
A minimap2 frontend for PacBio native data formats
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2024-12-13 |
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deepfplearn
|
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
|
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
|
public |
kmertools: DNA Vectorisation Tool
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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.
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2024-12-13 |
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ucsc-chainmergesort
|
public |
Combine sorted files into larger sorted file
|
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.
|
2024-12-13 |
|
iow
|
public |
Implementation of Balanced Parentheses
|
2024-12-13 |
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ibdmix
|
public |
ibdmix: estimate introgression by IBD
|
2024-12-13 |
|
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 |
|
dnp-corrprofile
|
public |
Profile of correlations between the patterns of dinucleotide frequency on forward and reverse strands
|
2024-12-13 |
|
maf2synteny
|
public |
A tool that postprocesses whole genome alignment (for two or more genomes) and produces coarse-grained synteny blocks.
|
2024-12-13 |
|
kalign3
|
public |
Kalign is a fast and accurate multiple sequence alignment algorithm.
|
2024-12-13 |
|
squizz
|
public |
Squizz is a sequence/alignment format checker, but it has some conversion capabilities too.
|
2024-12-13 |
|
hilive2
|
public |
Tool for real-time read alignment of Illumina sequencing data
|
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 |
|
lca
|
public |
LCA - Lowest Common Ancestor calculation tool
|
2024-12-13 |
|
cagee
|
public |
Analyzes changes in gene expression in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences
|
2024-12-13 |
|
lz4-bin
|
public |
Extremely Fast Compression Application
|
2024-12-13 |
|
polypolish
|
public |
Polishing genome assemblies with short reads.
|
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 |
|
virulign
|
public |
VIRULIGN is a tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins.
|
2024-12-13 |
|
nedbit-features-calculator
|
public |
Network diffusion and biology-informed topological features
|
2024-12-13 |
|
macs2
|
public |
Model Based Analysis for ChIP-Seq data
|
2024-12-13 |
|
prinseq-plus-plus
|
public |
PRINSEQ++ - Multi-threaded C++ sequence cleaning
|
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 |
|
yahs
|
public |
YaHS, yet another Hi-C scaffolding tool.
|
2024-12-13 |
|
fasta3
|
public |
The FASTA package - protein and DNA sequence similarity searching and alignment programs
|
2024-12-13 |
|
slamem
|
public |
slamem bioconda package from https://github.com/fjdf/slaMEM
|
2024-12-13 |
|
minimap
|
public |
Experimental tool to find approximate mapping positions between long sequences
|
2024-12-13 |
|
genomethreader
|
public |
GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.
|
2024-12-13 |
|
libdivsufsort
|
public |
No Summary
|
2024-12-13 |
