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brawn
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public |
A tool for handling repetitive insertions into sequence alignments.
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2024-11-28 |
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hicexplorer
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public |
Set of programs to process, analyze and visualize Hi-C and capture Hi-C data
|
2024-11-28 |
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perl-dbd-sqlite
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public |
Self Contained RDBMS in a DBI Driver
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2024-11-28 |
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perl-dbd-mysql
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public |
A MySQL driver for the Perl5 Database Interface (DBI)
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2024-11-28 |
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viral_consensus
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public |
Fast viral consensus genome reconstruction
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2024-11-28 |
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busco
|
public |
Assessment of assembly completeness using Universal Single Copy Orthologs.
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2024-11-28 |
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cpstools
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public |
CPStools is a package for analyzing chloroplast genome sequences.
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2024-11-28 |
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mosdepth
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public |
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
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2024-11-28 |
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fastplong
|
public |
Ultra-fast preprocessing and quality control for long-read sequencing data.
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2024-11-28 |
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nanomotif
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public |
Identifying methlyation motifs in nanopore data
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2024-11-28 |
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artic
|
public |
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore.
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2024-11-28 |
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strelka
|
public |
Strelka calls somatic and germline small variants from mapped sequencing reads
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2024-11-28 |
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repeatscout
|
public |
De novo identification of repeat families in large genomes.
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2024-11-28 |
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trf
|
public |
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
|
2024-11-28 |
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nseg
|
public |
nseg identifies and masks regions of low complexity in nucleic acid sequences
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2024-11-28 |
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oarfish
|
public |
oarfish is a tool for fast, accurate and versatile transcript quantification from long-read RNA-seq data
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2024-11-28 |
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ninja-nj
|
public |
Nearly Infinite Neighbor Joining Application
|
2024-11-28 |
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repeatmodeler
|
public |
RepeatModeler is a de-novo repeat family identification and modeling package.
|
2024-11-28 |
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pybigtools
|
public |
pybigtools: Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O
|
2024-11-28 |
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bracken
|
public |
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
|
2024-11-28 |
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bioconda-repodata-patches
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public |
generate tweaks to index metadata, hosted separately from anaconda.org index
|
2024-11-28 |
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bigtools
|
public |
Bigtools provides a high-level, performant API for reading and writing bigWig and bigBed files.
|
2024-11-27 |
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kraken2
|
public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
|
2024-11-27 |
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hisat2
|
public |
Graph-based alignment of next generation sequencing reads to a population of genomes.
|
2024-11-27 |
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nextflow
|
public |
A DSL for data-driven computational pipelines http://nextflow.io
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2024-11-27 |
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vclust
|
public |
Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes.
|
2024-11-27 |
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rsem
|
public |
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
|
2024-11-27 |
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mycotools
|
public |
Comparative genomics automation and standardization software.
|
2024-11-27 |
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hifiasm
|
public |
Haplotype-resolved assembler for accurate Hifi reads.
|
2024-11-27 |
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piscem
|
public |
piscem is a next-generation compacted colored de Bruijn Graph-based indexer and mapper
|
2024-11-27 |
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crisprme
|
public |
CRISPRme, tool package for CRISPR experiments assessment and analysis.
|
2024-11-27 |
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meraculous
|
public |
Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It's hybrid k-mer/read-based approach capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on a high-cpu cluster in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.
|
2024-11-27 |
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perl-extutils-cppguess
|
public |
guess C++ compiler and flags
|
2024-11-27 |
|
perl-set-intervaltree
|
public |
An interval tree implementation in PERL.
|
2024-11-27 |
|
control-freec
|
public |
Copy number and genotype annotation from whole genome and whole exome
sequencing data.
|
2024-11-27 |
|
clusty
|
public |
Clusty is a tool for large-scale data clustering.
|
2024-11-27 |
|
kmer-db
|
public |
Kmer-db is a fast and memory-efficient tool for estimating evolutionary distances.
|
2024-11-27 |
|
lz-ani
|
public |
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
|
2024-11-27 |
|
blast
|
public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
|
2024-11-27 |
|
phabox
|
public |
Virus identification and analysis tool set
|
2024-11-27 |
|
spatialleiden
|
public |
Implementation of multiplex Leiden for analysis of spatial omics data.
|
2024-11-27 |
|
snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2024-11-27 |
|
snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2024-11-27 |
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r-lisi
|
public |
This method was designed to assess how well mixed cells with different labels are in single cell RNAseq. This method uses the Inverse Simpson's Index to compute diversity of each cell's local neighborhood.
|
2024-11-27 |
|
bioconductor-biobase
|
public |
Biobase: Base functions for Bioconductor
|
2024-11-27 |
|
cojac
|
public |
Command-line tools to analyse co-occurrence of mutations on amplicons.
|
2024-11-27 |
|
lollipop
|
public |
A tool for Deconvolution for Wastewater Genomics
|
2024-11-27 |
|
sylph
|
public |
sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.
|
2024-11-27 |
|
mirscore
|
public |
miRScore: A rapid and precise microRNA validation tool
|
2024-11-27 |
|
mmseqs2
|
public |
MMseqs2: ultra fast and sensitive sequence search and clustering suite
|
2024-11-27 |
