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busco
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public |
Assessment of assembly completeness using Universal Single Copy Orthologs
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2024-09-17 |
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mummer
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public |
MUMmer is a system for rapidly aligning entire genomes
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2024-09-13 |
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bcftools
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public |
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
|
2024-09-12 |
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htslib
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public |
C library for high-throughput sequencing data formats.
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2024-09-12 |
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freebayes
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public |
Bayesian haplotype-based polymorphism discovery and genotyping
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2024-09-10 |
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snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2024-09-09 |
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bowtie2
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public |
A fast and sensitive gapped read aligner.
|
2024-08-21 |
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treetime
|
public |
Maximum-Likelihood dating and ancestral inference for phylogenetic trees
|
2024-08-11 |
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umi_tools
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public |
Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)
|
2024-08-05 |
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trinity
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public |
Trinity assembles transcript sequences from Illumina RNA-Seq data.
|
2024-08-04 |
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bracken
|
public |
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
|
2024-07-22 |
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gffcompare
|
public |
GffCompare by Geo Pertea
|
2024-07-18 |
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bamtools
|
public |
C++ API & command-line toolkit for working with BAM data
|
2024-07-10 |
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hicexplorer
|
public |
Set of programs to process, analyze and visualize Hi-C and capture Hi-C data
|
2024-06-28 |
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genomelake
|
public |
Simple and efficient random access to genomic data for deep learning models.
|
2024-06-12 |
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genometools-genometools
|
public |
GenomeTools genome analysis system.
|
2024-06-12 |
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peakachu
|
public |
Peak calling tool for CLIP-seq data.
|
2024-06-11 |
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htseq
|
public |
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
|
2024-06-11 |
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pbmm2
|
public |
A minimap2 frontend for PacBio native data formats
|
2024-06-11 |
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lofreq
|
public |
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
|
2024-06-08 |
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libmaus2
|
public |
collection of data structures and algorithms for NGS data
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2024-06-08 |
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bioconductor-deseq2
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public |
Differential gene expression analysis based on the negative binomial distribution
|
2024-05-30 |
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bioconductor-rtracklayer
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public |
R interface to genome annotation files and the UCSC genome browser
|
2024-05-27 |
|
bioconductor-hdf5array
|
public |
HDF5 backend for DelayedArray objects
|
2024-05-10 |
|
bioconductor-rhdf5
|
public |
R Interface to HDF5
|
2024-05-10 |
|
bioconductor-mzr
|
public |
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
|
2024-05-09 |
|
gtotree
|
public |
GToTree is a user-friendly workflow for phylogenomics.
|
2024-05-08 |
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stringtie
|
public |
StringTie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome.
|
2024-05-08 |
|
bioconductor-genomicranges
|
public |
Representation and manipulation of genomic intervals
|
2024-05-06 |
|
bioconductor-rhdf5lib
|
public |
hdf5 library as an R package
|
2024-05-06 |
|
bioconductor-iranges
|
public |
Foundation of integer range manipulation in Bioconductor
|
2024-05-02 |
|
bioconductor-xvector
|
public |
Foundation of external vector representation and manipulation in Bioconductor
|
2024-05-02 |
|
bioconductor-s4vectors
|
public |
Foundation of vector-like and list-like containers in Bioconductor
|
2024-05-01 |
|
snakedeploy
|
public |
Helper for deploying published Snakemake pipelines
|
2024-04-24 |
|
bioconductor-dexseq
|
public |
Inference of differential exon usage in RNA-Seq
|
2024-04-02 |
|
snippy
|
public |
Rapid bacterial SNP calling and core genome alignments
|
2024-03-15 |
|
deeptools
|
public |
A set of user-friendly tools for normalization and visualzation of deep-sequencing data
|
2024-03-08 |
|
scanpy-scripts
|
public |
Scripts for using scanpy from the command line
|
2024-02-21 |
|
raptor
|
public |
Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences
|
2024-01-17 |
|
bioconductor-genomeinfodb
|
public |
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
|
2023-12-06 |
|
bioconductor-genomeinfodbdata
|
public |
Species and taxonomy ID look up tables used by GenomeInfoDb
|
2023-12-05 |
|
bioconductor-data-packages
|
public |
A package to enable downloading and installation of Bioconductor data packages
|
2023-12-04 |
|
bioconductor-biocgenerics
|
public |
S4 generic functions used in Bioconductor
|
2023-12-04 |
|
gunc
|
public |
Python package for detection of chimerism and contamination in prokaryotic genomes.
|
2023-11-24 |
|
rmblast
|
public |
RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite.
|
2023-10-10 |
|
ngscheckmate
|
public |
Software package for identifying next generation sequencing (NGS) data files from the same individual.
|
2023-09-04 |
|
r-sceasy
|
public |
A package providing functions to convert between different single-cell data formats.
|
2023-07-19 |
|
flair
|
public |
Correction, isoform definition, and alternative splicing analysis of noisy reads (ONT and PacBio).
|
2023-07-16 |
|
trnascan-se
|
public |
tRNA detection in large-scale genomic sequences
|
2023-06-17 |
|
dipcall
|
public |
Dipcall is a reference-based variant calling pipeline for a pair of phased haplotype assemblies.
|
2023-06-16 |
