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.
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 | Linux 64
1.09 | 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 | Linux 64
0.6.2 | OS X INTEL
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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 | OS X INTEL
0.4.1 | Linux 64
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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 | OS X INTEL
0.9.3 | Linux 64
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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 | Linux 64
1.7 | OS X INTEL
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Aug 11 2023
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InSilicoSeq
A sequencing simulator.
Updated versions:
1.6.0 | Linux 64
1.6.0 | OS X INTEL
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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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