Apr 28 2023
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isoseq3
Scalable De Novo Isoform Discovery
Updated versions:
3.8.2 | Linux 64
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Apr 28 2023
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Minimap2
is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments.
Updated versions:
2.25 | Linux 64
2.25 | OS X INTEL
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Apr 21 2023
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OpenFold
a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.
Updated versions:
1.0.1 | Linux 64
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Apr 17 2023
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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 | Linux 64
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Apr 14 2023
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structure
Inference of population structure using multilocus genotype data
Updated versions:
2.3.4 | Linux 64
2.3.4 | OS X INTEL
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Apr 11 2023
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Foldseek
a program that enables fast and sensitive comparisons of large structure sets.
Updated versions:
5-53465f0 | Linux 64
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Apr 11 2023
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AmberTools
a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
Updated versions:
21 | Linux 64
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Apr 11 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:
2.1.6 | Linux 64
2.1.6 | OS X INTEL
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Apr 10 2023
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Segment Anything
(SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image.
Updated versions:
c3b8a88 | OS X INTEL
c3b8a88 | Linux 64
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Apr 07 2023
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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:
0.9.0 | OS X INTEL
0.9.0 | Linux 64
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Apr 06 2023
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VERSE
a versatile and efficient RNA-Seq read counting tool
Updated versions:
0.1.5 | Linux 64
0.1.5 | OS X INTEL
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Apr 06 2023
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regtools
is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
Updated versions:
1.0.0 | Linux 64
1.0.0 | OS X INTEL
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Apr 06 2023
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deSALT
De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
Updated versions:
1.5.6 | Linux 64
1.5.6 | OS X INTEL
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Apr 05 2023
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Salmon
a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses algorithms to provide very quick, accurate expression estimates using little memory and performs inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.
Updated versions:
1.10.1 | Linux 64
1.10.1 | OS X INTEL
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Apr 05 2023
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pangolin
(Phylogenetic Assignment of Named Global Outbreak LINeages) software package for assigning SARS-CoV-2 genome sequences to global lineages.
Updated versions:
4.2 | Linux 64
4.2 | OS X INTEL
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Apr 05 2023
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StringTie
a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).
Updated versions:
2.2.1 | Linux 64
2.2.1 | OS X INTEL
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Apr 04 2023
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pbipa
IPA HiFi Genome Assembler
Updated versions:
1.8.0 | Linux 64
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Apr 04 2023
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lordec
A hybrid error correction program for long, PacBio reads
Updated versions:
0.9 | Linux 64
0.9 | OS X INTEL
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Apr 04 2023
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Canu
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing. Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly. The correction phase will improve the accuracy of bases in reads.
Updated versions:
2.2 | Linux 64
2.2 | OS X INTEL
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Apr 03 2023
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hera
a bioinformatics tool that helps analyze RNA-seq data, providing base-to-base alignment BAM files, transcript abundance estimation, and fusion gene detection.
Updated versions:
1.1 | OS X INTEL
1.1 | Linux 64
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Apr 03 2023
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Ryuto
Network-Flow based Transcriptome Reconstruction
Updated versions:
1.6.3 | OS X INTEL
1.6.3 | Linux 64
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Apr 03 2023
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MultiQC
aggregates results from bioinformatics analyses across many samples into a single report.
Updated versions:
1.14 | Linux 64
1.14 | OS X INTEL
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Apr 03 2023
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PCAone
Principal Component Analysis All in One
Updated versions:
0.3.2 | Linux 64
0.3.2 | OS X INTEL
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