Oct 31 2024
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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:
4.6.1.0 | Linux 64
4.6.1.0 | OS X INTEL
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Oct 29 2024
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AlphaFold
an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:
2.3.2_20241024 | Linux 64
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Oct 28 2024
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Luna
is an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.
Updated versions:
1.0.0-lgbm | Linux 64
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Oct 18 2024
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RBPBench
RBPBench is multi-function tool to evaluate CLIP-seq and other genomic region data using a comprehensive collection of known RNA-binding protein (RBP) binding motifs.
Updated versions:
1.0.1 | OS X INTEL
1.0.1 | Linux 64
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Oct 17 2024
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DNAscent
DNAscent is software designed to detect the base analogues BrdU and EdU in single molecules of DNA sequenced on the Oxford Nanopore platform
Updated versions:
4.0.3 | Linux 64
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Oct 07 2024
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gsMap
gsMap (genetically informed spatial mapping of cells for complex traits) integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner.
Updated versions:
1.70 | Linux 64
1.70 | OS X INTEL
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Oct 07 2024
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strobealign
a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy, see the performance evaluation.
Updated versions:
0.14.0 | Linux 64
0.14.0 | OS X INTEL
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Oct 04 2024
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LazyPredict
Lazy Predict helps build a lot of basic models without much code and helps understand which models works better without any parameter tuning.
Updated versions:
0.2.12 | OS X INTEL
0.2.12 | Linux 64
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Oct 04 2024
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tidk
Identify and find telomeres, or telomeric repeats in a genome.
Updated versions:
0.2.63 | Linux 64
0.2.63 | OS X INTEL
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Oct 03 2024
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LongReadSum
LongReadSum supports FASTA, FASTQ, BAM, FAST5, and sequencing_summary.txt file formats for quick generation of QC data in HTML and text format.
Updated versions:
1.3.1 | Linux 64
1.3.1 | OS X INTEL
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Oct 02 2024
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smoothxg
Local reconstruction of variation graphs using partial order alignment.
Pangenome graphs built from raw sets of alignments may have complex local structures generated by common patterns of genome variation. smoothxg can be used to extract the consensus pangenome graph by applying the heaviest bundle algorithm to each chain.
Updated versions:
0.6.7 | Linux 64
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Oct 02 2024
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falco
is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
Updated versions:
1.2.1 | OS X INTEL
1.2.1 | Linux 64
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Oct 02 2024
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Recentrifuge
Robust comparative analysis and contamination removal for metagenomics
Updated versions:
1.13.1 | OS X INTEL
1.13.1 | Linux 64
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Oct 02 2024
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epic2
Ultraperformant Chip-Seq broad domain finder based on SICER.
Updated versions:
0.0.52 | Linux 64
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Oct 02 2024
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hifiasm_meta
Metagenome assembler for Hifi reads, based on hifiasm.
Updated versions:
hamtv0.3.1 | OS X INTEL
hamtv0.3.1 | Linux 64
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Oct 02 2024
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panacus
a counting tool for pangenome graphs. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.
Updated versions:
0.2.4 | Linux 64
0.2.4 | OS X INTEL
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Oct 02 2024
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gappa
Genesis Applications for Phylogenetic Placement Analysis
Updated versions:
0.8.5 | Linux 64
0.8.5 | OS X INTEL
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Oct 01 2024
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VeryFastTree
a new tool designed for efficient phylogenetic tree inference, specifically tailored to handle massive taxonomic datasets. It is a highly-tuned implementation based on the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments.
Updated versions:
4.0.4 | OS X INTEL
4.0.4 | Linux 64
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Oct 01 2024
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Spark
a multi-language engine for executing data engineering, data science, and machine learning on single-node machines or clusters.
Updated versions:
3.5.3 | Linux 64
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Oct 01 2024
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covtobed
a tool to generate BED coverage tracks from BAM files.
It reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range.
Updated versions:
1.3.5 | OS X INTEL
1.3.5 | Linux 64
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Oct 01 2024
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EPA-ng
a complete rewrite of the Evolutionary Placement Algorithm (EPA), previously implemented in RAxML. It uses libpll and pll-modules to perform maximum likelihood-based phylogenetic placement of genetic sequences on a user-supplied reference tree and alignment.
Updated versions:
0.3.8 | Linux 64
0.3.8 | OS X INTEL
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