Jul 30 2021
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selscan
a program to calculate EHH-based scans for positive selection in genomes.
Updated versions:
1.2.0a | OS X INTEL
1.2.0a | Linux 64
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Jul 30 2021
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TideHunter
efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain.
Updated versions:
1.4.3 | Linux 64
1.4.3 | OS X INTEL
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Jul 30 2021
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Crumble
controllable lossy compression of BAM/CRAM files.
Updated versions:
0.8.3 | OS X INTEL
0.8.3 | Linux 64
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Jul 30 2021
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pybedtools
pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
Updated versions:
0.8.2 | OS X INTEL
0.8.2 | Linux 64
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Jul 30 2021
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Dextractor
bax file decoder and data compressor.
Updated versions:
1.0p2 | OS X INTEL
1.0p2 | Linux 64
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Jul 30 2021
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RAxML-NG
a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
Updated versions:
1.0.3 | Linux 64
1.0.3 | OS X INTEL
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Jul 30 2021
|
TreeBeST
(Tree Building guided by Species Tree) is a versatile program that builds, manipulates and displays phylogenetic trees.
Updated versions:
1.9.2 | Linux 64
1.9.2 | OS X INTEL
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Jul 30 2021
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downpore
a suite of tools for use in genome assembly and consensus.
Updated versions:
0.3.4 | OS X INTEL
0.3.4 | Linux 64
|
Jul 28 2021
|
fqtools
an efficient FASTQ manipulation suite.
Updated versions:
2.1 | Linux 64
2.1 | OS X INTEL
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Jul 27 2021
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FastME
FastME provides distance algorithms to infer phylogenies.
Updated versions:
2.1.6.1 | Linux 64
2.1.6.1 | OS X INTEL
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Jul 27 2021
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fastq-scan
fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.
Updated versions:
0.4.4 | OS X INTEL
0.4.4 | Linux 64
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Jul 26 2021
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abPOA
an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation.
Updated versions:
1.2.5 | Linux 64
1.2.5 | OS X INTEL
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Jul 26 2021
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srprism
Short Read Alignment Tool
Updated versions:
2.4.24 | OS X INTEL
2.4.24 | Linux 64
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Jul 26 2021
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HULK
(Histosketching Using Little Kmers) a tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
Updated versions:
1.0.0 | Linux 64
1.0.0 | OS X INTEL
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Jul 26 2021
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SKESA
(Strategic Kmer Extension for Scrupulous Assemblies) a de-novo sequence read assembler for microbial genomes.
Updated versions:
2.4.0 | Linux 64
2.4.0 | OS X INTEL
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Jul 26 2021
|
TN93
a fast distance calculator that computes pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.
Updated versions:
1.0.6 | Linux 64
1.0.6 | OS X INTEL
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Jul 23 2021
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FastANI
developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
Updated versions:
1.32 | Linux 64
1.32 | OS X INTEL
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Jul 23 2021
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OCOCO
the first program capable of inferring variants in a real-time, as read alignments are fed in. Ococo inputs unsorted alignments from a stream and infers single-nucleotide variants, together with a genomic consensus, using statistics stored in compact several-bit counters.
Updated versions:
0.1.2.4 | OS X INTEL
0.1.2.4 | Linux 64
|
Jul 23 2021
|
PRANK
a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.
Updated versions:
v.170427 | Linux 64
v.170427 | OS X INTEL
|
Jul 23 2021
|
daligner
finds all significant local alignments between reads.
Updated versions:
1.0.20200322 | OS X INTEL
1.0.20200322 | Linux 64
|
Jul 23 2021
|
scrm
a coalescent simulator for biological sequences.
Updated versions:
1.7.4 | OS X INTEL
1.7.4 | Linux 64
|
Jul 22 2021
|
CLARK
fast, accurate and versatile k-mer based classification system.
Updated versions:
1.2.6.1 | Linux 64
1.2.6.1 | OS X INTEL
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Jul 22 2021
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Lighter
a kmer-based error correction method for whole genome sequencing data.
Updated versions:
1.1.2 | OS X INTEL
1.1.2 | Linux 64
|
Jul 22 2021
|
SNP-sites
rapidly extracts SNPs from a multi-FASTA alignment.
Updated versions:
2.5.1 | OS X INTEL
2.5.1 | Linux 64
|
Jul 21 2021
|
Longshot
a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).
Updated versions:
0.4.1 | OS X INTEL
0.4.1 | Linux 64
|
Jul 21 2021
|
RNA-SeQC
fast, efficient RNA-Seq metrics for quality control and process optimization.
Updated versions:
2.3.5 | Linux 64
2.3.5 | OS X INTEL
|
Jul 21 2021
|
kallisto
a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Updated versions:
0.46.2 | OS X INTEL
0.46.2 | Linux 64
|
Jul 20 2021
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.13 | Linux 64
|
Jul 19 2021
|
OpenMPI
an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.
Updated versions:
4.1.1 | Linux 64
|
Jul 19 2021
|
Tracy
basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files.
Updated versions:
0.6.1 | Linux 64
0.6.1 | OS X INTEL
|
Jul 19 2021
|
Filtlong
a tool for filtering long reads by quality.
Updated versions:
0.2.1 | OS X INTEL
0.2.1 | Linux 64
|
Jul 19 2021
|
Cuttlefish
a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s).
Updated versions:
1.0.0 | Linux 64
1.0.0 | OS X INTEL
|
Jul 15 2021
|
UShER
a program that rapidly places new samples onto an existing phylogeny using maximum parsimony. It is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny.
Updated versions:
0.3.5 | Linux 64
0.3.5 | OS X INTEL
|
Jul 15 2021
|
Subread
comprises a suite of software programs for processing next-gen sequencing read data including
- Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
- featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins.
- Sublong: a long-read aligner that is designed based on seed-and-vote.
- exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.
Updated versions:
2.0.3 | Linux 64
2.0.3 | OS X INTEL
|
Jul 15 2021
|
UMI-tools
tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
Updated versions:
1.1.2 | OS X INTEL
1.1.2 | Linux 64
|
Jul 09 2021
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.13 | OS X INTEL
|
Jul 05 2021
|
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:
1.5.1 | Linux 64
1.5.1 | OS X INTEL
|