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mummer
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public |
MUMmer is a system for rapidly aligning entire genomes
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2024-12-13 |
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ucsc-hgfakeagp
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public |
Create fake AGP file by looking at N's
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2024-12-13 |
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seqprep
|
public |
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
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2024-12-13 |
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ucsc-catuncomment
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public |
Concatenate input removing lines that start with '#'
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2024-12-13 |
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ucsc-paratestjob
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public |
version 12.18
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2024-12-13 |
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ucsc-bigbedtobed
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public |
Convert from bigBed to ascii bed format.
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2024-12-13 |
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ucsc-positionaltblcheck
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public |
check that positional tables are sorted
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2024-12-13 |
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ucsc-blat
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public |
Standalone BLAT v. 39x1 fast sequence search command line tool.
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2024-12-13 |
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ucsc-maketablelist
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public |
create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE)
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2024-12-13 |
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fido
|
public |
No Summary
|
2024-12-13 |
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sickle-trim
|
public |
Windowed Adaptive Trimming for fastq files using quality
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2024-12-13 |
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ucsc-twobittofa
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public |
Convert all or part of .2bit file to fasta.
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2024-12-13 |
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clustalo
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public |
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
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2024-12-13 |
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ucsc-chainsort
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public |
Sort chains. By default sorts by score.
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2024-12-13 |
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ucsc-localtime
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public |
convert unix timestamp to date string
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2024-12-13 |
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ucsc-rmfadups
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public |
remove duplicate records in FA file
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2024-12-13 |
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satrap
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public |
A SOLiD assembly translation program.
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2024-12-13 |
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ucsc-pslcat
|
public |
concatenate psl files
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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
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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.
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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
|
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
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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.
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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
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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.
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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 |
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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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phipack
|
public |
Simple, rapid, and statistically efficient test for recombination.
|
2024-12-13 |
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ucsc-fasize
|
public |
print total base count in fa files.
|
2024-12-13 |
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samblaster
|
public |
Mark duplicates in and extract discordant and split reads from SAM files.
|
2024-12-13 |
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ucsc-axtswap
|
public |
Swap source and query in an axt file
|
2024-12-13 |
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ucsc-randomlines
|
public |
Pick out random lines from file
|
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
|
2024-12-13 |
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ucsc-fastqstatsandsubsample
|
public |
Go through a fastq file doing sanity checks and collecting stats
|
2024-12-13 |
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pbmm2
|
public |
A minimap2 frontend for PacBio native data formats
|
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
|
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 |
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gocr
|
public |
GOCR is an OCR (Optical Character Recognition) program
|
2024-12-13 |
