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genomedata
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public |
Tools for accessing large amounts of genomic data
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2024-09-29 |
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trnascan-se
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public |
tRNA detection in large-scale genomic sequences
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2024-09-27 |
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infernal
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public |
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
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2024-09-27 |
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kallisto
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public |
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
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2024-09-25 |
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planemo
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public |
Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
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2024-09-24 |
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guidescan
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public |
GuideScan is a tool for genome-wide CRISPR guide RNA (gRNA) design and analysis in custom genomes.
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2024-09-23 |
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checkm-genome
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public |
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
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2024-09-23 |
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percolator
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public |
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
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2024-09-20 |
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fastq-screen
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public |
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
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2024-09-20 |
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blast-legacy
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public |
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
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2024-09-20 |
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fiji
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public |
Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
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2024-09-19 |
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kraken2
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public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
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2024-09-19 |
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jalview
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public |
Jalview is a free program for multiple sequence alignment editing, visualisation, analysis and figure generation.
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2024-09-19 |
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r-wgcna
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public |
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
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2024-09-18 |
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intarna
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public |
Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites
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2024-09-18 |
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repeatmasker
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public |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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2024-09-17 |
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genomepy
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public |
Install and use genomes & gene annotations the easy way!
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2024-09-17 |
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tracy
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public |
Basecalling, alignment, assembly and deconvolution of Sanger chromatogram trace files
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2024-09-17 |
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vcflib
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public |
Command-line tools for manipulating VCF files.
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2024-09-17 |
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mirtop
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public |
Small RNA-seq annotation.
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2024-09-17 |
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snp-pileup
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public |
Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets
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2024-09-17 |
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cnv_facets
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public |
Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data
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2024-09-17 |
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alfred
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public |
BAM alignment statistics, feature counting and feature annotation
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2024-09-16 |
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bx-python
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public |
Tools for manipulating biological data, particularly multiple sequence alignments
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2024-09-16 |
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pronto
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public |
Python frontend to ontologies
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2024-09-15 |
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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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bioconvert
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public |
Convert between bioinformatics formats
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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.
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2024-09-12 |
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samtools
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public |
Tools for dealing with SAM, BAM and CRAM files
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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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gdc-client
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public |
GDC Data Transfer Tool
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2024-09-11 |
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mcl
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public |
MCL - a cluster algorithm for graphs
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2024-09-11 |
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synapseclient
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public |
Python client for Synapse
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2024-09-10 |
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moods
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public |
MOODS: Motif Occurrence Detection Suite
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2024-09-10 |
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toulligqc
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public |
A post sequencing QC tool for Oxford Nanopore sequencers.
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2024-09-10 |
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sra-tools
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public |
The SRA Toolkit and SDK from NCBI.
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2024-09-10 |
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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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ncbi-vdb
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public |
SRA tools database engine
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2024-09-10 |
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perl-mce
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public |
Many-Core Engine for Perl providing parallel processing capabilities
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2024-09-10 |
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perl-mce-shared
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public |
MCE extension for sharing data supporting threads and processes
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2024-09-10 |
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graphmap
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public |
A highly sensitive and accurate mapper for long, error-prone reads
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2024-09-09 |
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truvari
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public |
Structural variant comparison tool for VCFs
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2024-09-09 |
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eigensoft
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public |
The EIGENSOFT package implements methods for analzing population structure and performing stratification correction
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2024-09-09 |
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scnic
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public |
SCNIC: Sparse Cooccurence Network Investigation for Compositional data
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2024-09-06 |
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egglib
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public |
Evolutionary Genetics and Genomics Library. EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, and coalescent simulations. EggLib is a flexible Python module with a performant underlying C++ library and allows fast and intuitive development of Python programs and scripts.
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2024-09-06 |
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python-edlib
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public |
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
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2024-09-05 |
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clipandmerge
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public |
Clip&Merge is a tool to clip off adapters from sequencing reads and merge overlapping paired end reads together.
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2024-09-05 |
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dedup
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public |
DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
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2024-09-05 |
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perl-graph
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public |
a Perl extension for keeping data partially sorted
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2024-09-02 |
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tigmint
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public |
Correct misassemblies using linked or long reads
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2024-09-01 |
