Aug 29 2023
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deepTools
a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
Updated versions:
3.5.3 | OS X INTEL
3.5.3 | Linux 64
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Aug 28 2023
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Snakemake
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
Updated versions:
7.32.3 | Linux 64
7.32.3 | OS X INTEL
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Aug 22 2023
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DIAMOND
a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
Updated versions:
2.1.8 | Linux 64
2.1.8 | OS X INTEL
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Aug 22 2023
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corset
Software for clustering de novo assembled transcripts and counting overlapping reads.
Updated versions:
1.09 | OS X INTEL
1.09 | Linux 64
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Aug 21 2023
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R-pkgs-Biogrids
contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions:
r4.2.3-20230807 | Linux 64
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Aug 21 2023
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R
a free software environment for statistical computing and graphics.
Updated versions:
4.2.3 | OS X INTEL
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Aug 17 2023
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spaceranger
Visium Spatial Software Suite for analyzing and visualizing spatial gene and protein expression data
Updated versions:
2.1.0 | Linux 64
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Aug 16 2023
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EMA
Fast & accurate alignment of barcoded short-reads
Updated versions:
0.6.2 | OS X INTEL
0.6.2 | Linux 64
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Aug 16 2023
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lastz
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
Updated versions:
1.04.22 | Linux 64
1.04.22 | OS X INTEL
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Aug 16 2023
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vcf2parquet
Convert a vcf in parquet.
Updated versions:
0.4.1 | Linux 64
0.4.1 | OS X INTEL
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Aug 16 2023
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isoseq3
Scalable De Novo Isoform Discovery
Updated versions:
4.0.0 | Linux 64
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Aug 16 2023
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PFP
Tool to build the parse and the dictionary for VCF files using the approach described in Prefix-Free Parsing for Building Big BWTs
Updated versions:
0.3.9 | Linux 64
0.3.9 | OS X INTEL
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Aug 16 2023
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KMCP
accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Updated versions:
0.9.3 | Linux 64
0.9.3 | OS X INTEL
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Aug 15 2023
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abismal
abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads
Updated versions:
3.2.0 | Linux 64
3.2.0 | OS X INTEL
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Aug 15 2023
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msamtools
microbiome-related extension to samtools
Updated versions:
1.1.3 | Linux 64
1.1.3 | OS X INTEL
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Aug 15 2023
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LevioSAM2
Fast and accurate coordinate conversion between assemblies
Updated versions:
0.4.1 | Linux 64
0.4.1 | OS X INTEL
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Aug 14 2023
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GATK
(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Updated versions:
4.4.0.0 | Linux 64
4.4.0.0 | OS X INTEL
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Aug 11 2023
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STAR
(Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
Updated versions:
2.7.10b | OS X INTEL
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Aug 11 2023
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sdm
simple demultiplex tool for FASTQ demultiplexing and dereplication.
Updated versions:
2.10 | Linux 64
2.10 | OS X INTEL
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Aug 11 2023
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platon
Plasmid contig classification and characterization for short read draft assemblies.
Updated versions:
1.7 | OS X INTEL
1.7 | Linux 64
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Aug 11 2023
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InSilicoSeq
A sequencing simulator.
Updated versions:
1.6.0 | OS X INTEL
1.6.0 | Linux 64
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Aug 10 2023
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dnmtools
a set of tools for analyzing DNA methylation data from bisulfite sequencing
Updated versions:
1.3.0 | OS X INTEL
1.3.0 | Linux 64
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Aug 04 2023
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AGAT
(Another Gff Analysis Toolkit) a suite of tools to handle gene annotations in any GTF/GFF format.
Updated versions:
1.2.0 | Linux 64
1.2.0 | OS X INTEL
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