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ucsc-mafspecieslist
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public |
Scan maf and output all species used in it.
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2024-12-14 |
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ucsc-pslrc
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public |
reverse-complement psl
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2024-12-14 |
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meraculous
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public |
Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It's hybrid k-mer/read-based approach capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on a high-cpu cluster in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.
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2024-12-14 |
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hisat2
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public |
Graph-based alignment of next generation sequencing reads to a population of genomes.
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2024-12-14 |
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ucsc-bedgraphpack
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public |
Pack together adjacent records representing same value.
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2024-12-14 |
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perl-convert-binary-c
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public |
Binary Data Conversion using C Types
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2024-12-14 |
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sketchy
|
public |
Real-time lineage hashing and genotyping of bacterial pathogens
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2024-12-14 |
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parafly
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public |
Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported.
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2024-12-14 |
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phyml
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public |
Phylogenetic estimation using (Maximum) Likelihood
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2024-12-14 |
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ucsc-maftoaxt
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public |
Convert from maf to axt format
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2024-12-14 |
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irfinder
|
public |
Intron Retention Finder
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2024-12-14 |
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ucsc-genepredtobed
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public |
Convert from genePred to bed format. Does not yet handle genePredExt
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2024-12-14 |
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tntblast
|
public |
Searching DNA/RNA sequence databases with PCR and/or probe queries
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2024-12-14 |
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ucsc-chaincleaner
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public |
Remove chain-breaking alignments from chains that break nested chains.
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2024-12-14 |
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ucsc-chaintopslbasic
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public |
Basic conversion chain file to psl format
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2024-12-14 |
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structure
|
public |
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
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2024-12-14 |
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sfs_code
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public |
This article introduces a new forward population genetic simulation program that can efficiently generate samples from populations with complex demographic histories under various models of natural selection. The program (SFS_CODE) is highly flexible, allowing the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and allows for insertions and deletions. Each locus can be annotated as either coding or non-coding, sex-linked or autosomal, selected or neutral, and have an arbitrary linkage structure (from completely linked to independent). © The Author 2008. Published by Oxford University Press. All rights reserved.
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2024-12-13 |
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msweep
|
public |
mSWEEP - bacterial community composition estimation from pseudoalignments
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2024-12-13 |
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r-chbutils
|
public |
Useful utility functions used at the Harvard Chan School Bioinformatics core
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2024-12-13 |
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deploid
|
public |
A software that deconvolutes mixed genomes with unknown proportions.
|
2024-12-13 |
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ucsc-bigwigcorrelate
|
public |
Correlate bigWig files, optionally only on target regions.
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2024-12-13 |
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ucsc-ticktodate
|
public |
Convert seconds since 1970 to time and date
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2024-12-13 |
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king
|
public |
`Kinship-based INference for Gwas (KING) is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study <http://people.virginia.edu/~wc9c/KING/>`_
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2024-12-13 |
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kaiju
|
public |
Fast and sensitive taxonomic classification for metagenomics
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2024-12-13 |
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gfastats
|
public |
The swiss army knife for genome assembly
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2024-12-13 |
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gfmix
|
public |
Accelerated Estimation of Frequency Classes in Site-heterogeneous Profile Mixture Models
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2024-12-13 |
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r-rubic
|
public |
No Summary
|
2024-12-13 |
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smhasher
|
public |
No Summary
|
2024-12-13 |
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ucsc-chromgraphtobin
|
public |
Make binary version of chromGraph.
|
2024-12-13 |
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ucsc-chainprenet
|
public |
Remove chains that don't have a chance of being netted
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2024-12-13 |
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zerone
|
public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
|
2024-12-13 |
|
rpsbproc
|
public |
RpsbProc, the post-RPSBLAST Processing Utility.
|
2024-12-13 |
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perl-math-cdf
|
public |
Generate probabilities and quantiles from several statistical probability functions
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2024-12-13 |
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wise2
|
public |
The Wise2.4 package is the "revival" release of Wise2
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2024-12-13 |
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kart
|
public |
Kart: a divide-and-conquer algorithm for NGS read alignment
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2024-12-13 |
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sage-proteomics
|
public |
Proteomics searching so fast it feels like magic.
|
2024-12-13 |
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narfmap
|
public |
NARFMAP is a fork of the Dragen mapper/aligner Open Source Software.
|
2024-12-13 |
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takeabreak
|
public |
tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes
|
2024-12-13 |
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gretl
|
public |
gretl is a tool to compute a range of statistics on variation graphs in gfa format.
|
2024-12-13 |
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dechat
|
public |
Repeat and haplotype aware error correction in nanopore sequencing reads with Dechat
|
2024-12-13 |
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ucsc-chainfilter
|
public |
Filter chain files. Output goes to standard out.
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2024-12-13 |
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groot
|
public |
A tool for resistome profiling of metagenomic samples.
|
2024-12-13 |
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prodigal
|
public |
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
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2024-12-13 |
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hifiasm_meta
|
public |
Metagenome assembler for Hifi reads, based on hifiasm.
|
2024-12-13 |
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ucsc-wigtobigwig
|
public |
Convert ascii format wig file (in fixedStep, variableStep).
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2024-12-13 |
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pytabix
|
public |
Fast random access to sorted files compressed with bgzip and indexed by tabix.
|
2024-12-13 |
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ucsc-bigwigsummary
|
public |
Extract summary information from a bigWig file.
|
2024-12-13 |
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haplomap
|
public |
Haplotype-based computational genetic mapping.
|
2024-12-13 |
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fxtract
|
public |
Extract sequences from a fastx file given a subsequence or identifier.
|
2024-12-13 |
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ucsc-psldropoverlap
|
public |
deletes all overlapping self alignments.
|
2024-12-13 |
