May 30 2023
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Control-FREEC
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Updated versions:
11.6 | Linux 64
11.6 | OS X INTEL
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May 26 2023
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TakeABreak
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
Updated versions:
1.1.2 | Linux 64
1.1.2 | OS X INTEL
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May 26 2023
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GSearch
is an ultra-fast and scalable microbial genome search program based on MinHash-like metric and graph-based approximate nearest neighbor search
Updated versions:
0.1.2 | Linux 64
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May 26 2023
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unikmer
toolkit for k-mer with taxonomic information
Updated versions:
0.19.1 | Linux 64
0.19.1 | OS X INTEL
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May 22 2023
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medaka
a tool to create consensus sequences and variant calls from nanopore sequencing data.
Updated versions:
1.8.0 | Linux 64
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May 22 2023
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Metaphor
Metagenomic Pipeline for Short Reads
Updated versions:
1.7.7 | Linux 64
1.7.7 | OS X INTEL
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May 19 2023
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ChIPs
ChIPs is a tool for simulating ChIP-sequencing experiments.
Updated versions:
2.4 | Linux 64
2.4 | OS X INTEL
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May 19 2023
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MetaGraph
The MetaGraph framework allows for indexing and analysis of very large biological sequence collections, producing compressed indexes that can represent several petabases of input data. The indexes can be efficiently queried with any query sequence of interest.
Updated versions:
0.3.6 | Linux 64
0.3.6 | OS X INTEL
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May 19 2023
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dEploid
deconvolutes mixed genomes with unknown proportions.
Updated versions:
0.5 | Linux 64
0.5 | OS X INTEL
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May 17 2023
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GCEN
a command-line toolkit that allows biologists to easily build gene co-expression network and predict gene function, especially in RNA-Seq research or lncRNAs annotation
Updated versions:
0.6.3 | OS X INTEL
0.6.3 | Linux 64
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May 17 2023
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Captus
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
Updated versions:
0.9.91 | Linux 64
0.9.91 | OS X INTEL
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May 17 2023
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SRA Toolkit
(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Updated versions:
3.0.5 | Linux 64
3.0.5 | OS X INTEL
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May 15 2023
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shark
Mapping-free filtering of useless RNA-Seq reads
Updated versions:
1.2.0 | Linux 64
1.2.0 | OS X INTEL
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May 14 2023
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CellProfiler
a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
Updated versions:
3.1.3 | Linux 64
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May 12 2023
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YaHS
YaHS, yet another Hi-C scaffolding tool
Updated versions:
1.2a.2 | Linux 64
1.2a.2 | OS X INTEL
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May 12 2023
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SpydrPick
Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure
Updated versions:
1.2.0 | Linux 64
1.2.0 | OS X INTEL
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May 11 2023
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umis
tools for processing UMI RNA-tag data.
Updated versions:
1.0.9 | Linux 64
1.0.9 | OS X INTEL
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May 09 2023
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CellProfiler
a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
Updated versions:
4.2.5 | Linux 64
4.2.5 | OS X INTEL
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May 09 2023
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bedtools
a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Updated versions:
2.31.0 | Linux 64
2.31.0 | OS X INTEL
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May 08 2023
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LCA
Lowest Common Ancestor calculation tool
Updated versions:
0.24 | OS X INTEL
0.24 | Linux 64
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May 08 2023
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fastq-dl
A tool to download FASTQs associated with Study, Experiment, or Run accessions.
Updated versions:
2.0.1 | Linux 64
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May 08 2023
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TreeTime
provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.
Updated versions:
0.10.0 | Linux 64
0.10.0 | OS X INTEL
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May 04 2023
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3D Slicer
is a free and open-source platform for analyzing and understanding medical image data.
Updated versions:
4.10.2 | OS X INTEL
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May 01 2023
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Jellyfish
a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
Updated versions:
2.3.0 | Linux 64
2.3.0 | OS X INTEL
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May 01 2023
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km
software for RNA-seq investigation using k-mer decomposition
Updated versions:
2.1.1 | Linux 64
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