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sawfish
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public |
Structural variant discovery and genotyping from mapped PacBio HiFi data
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2024-08-22 |
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r-buencolors
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public |
R utility package for color mapping and plot aesthetics.
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2024-08-22 |
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pyseer
|
public |
Sequence Element Enrichment Analysis (SEER), python implementation
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2024-08-22 |
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pbstarphase
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public |
A phase-aware pharmacogenomic diplotyper for PacBio sequencing data
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2024-08-21 |
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gw
|
public |
View genomic sequencing data and vcf files
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2024-08-21 |
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pysradb
|
public |
Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO
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2024-08-21 |
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cami-amber
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public |
AMBER: Assessment of Metagenome BinnERs
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2024-08-21 |
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multiqc
|
public |
Create aggregate bioinformatics analysis reports across many samples and tools.
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2024-08-21 |
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assembly_finder
|
public |
Snakemake-powered cli pipeline to download genomes with NCBI datasets
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2024-08-21 |
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cami-opal
|
public |
OPAL assesses and compares the performance of taxonomic metagenome profilers.
|
2024-08-21 |
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snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
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2024-08-21 |
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snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2024-08-21 |
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gmap
|
public |
Genomic mapping and alignment program for mRNA and EST sequences.
|
2024-08-21 |
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r-signac
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public |
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>.
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2024-08-21 |
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whatshap
|
public |
phase genomic variants using DNA sequencing reads (haplotype assembly)
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2024-08-21 |
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r-quilt
|
public |
Rapid and accurate genotype imputation from low coverage short read, long read, and cell free DNA sequence
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2024-08-21 |
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python-hyphy-python
|
public |
HyPhy package interface library
|
2024-08-21 |
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kleborate
|
public |
Kleborate: a tool for typing and screening pathogen genome assemblies
|
2024-08-21 |
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bbmap
|
public |
BBMap is a short read aligner, as well as various other bioinformatic tools.
|
2024-08-21 |
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trackplot
|
public |
The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.
|
2024-08-21 |
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strdust
|
public |
Tandem repeat genotyper for long reads.
|
2024-08-21 |
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mquad
|
public |
MQuad: Mixture Model for Mitochondrial Mutation detection in single-cell omics data.
|
2024-08-21 |
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fast-edit-distance
|
public |
A implementation of edit distance with improved runtime.
|
2024-08-21 |
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bbmix
|
public |
BBMix: inference of beta-binomial mixture model
|
2024-08-21 |
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cyvcf2
|
public |
A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files
|
2024-08-21 |
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pgenlib
|
public |
Python wrapper for pgenlib's basic reader and writer.
|
2024-08-21 |
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gmwi2
|
public |
Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles
|
2024-08-21 |
|
bowtie2
|
public |
A fast and sensitive gapped read aligner.
|
2024-08-21 |
|
fgpyo
|
public |
Python bioinformatics and genomics library
|
2024-08-21 |
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vcfsim
|
public |
Script for generating simulated VCF's leveraging a coalescent simulating backend.
|
2024-08-21 |
|
fqtk
|
public |
A toolkit for working with FASTQ files.
|
2024-08-21 |
|
ensembl-utils
|
public |
Ensembl Python general-purpose utils
|
2024-08-21 |
|
last
|
public |
LAST finds & aligns related regions of sequences.
|
2024-08-20 |
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cutadapt
|
public |
Trim adapters from high-throughput sequencing reads
|
2024-08-20 |
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muscle
|
public |
MUSCLE: multiple sequence alignment with high accuracy and high throughput
|
2024-08-20 |
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synapseclient
|
public |
Python client for Synapse
|
2024-08-20 |
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ucsc-bigwigmerge
|
public |
Merge together multiple bigWigs into a single output bedGraph.
|
2024-08-20 |
|
ropebwt3
|
public |
Constructs the FM-index of a large DNA sequence set and searches for matches against the FM-index.
|
2024-08-20 |
|
earlgrey
|
public |
Earl Grey: A fully automated TE curation and annotation pipeline
|
2024-08-20 |
|
mgems
|
public |
mGEMS - sequencing data binning based on probabilistic classification
|
2024-08-20 |
|
ena-webin-cli
|
public |
Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI).
|
2024-08-20 |
|
snakemake-storage-plugin-gcs
|
public |
A Snakemake storage plugin for Google Cloud Storage
|
2024-08-20 |
|
ms2query
|
public |
Reliable and fast MS/MS spectral based analogue search
|
2024-08-20 |
|
msweep
|
public |
mSWEEP - bacterial community composition estimation from pseudoalignments
|
2024-08-20 |
|
dnaio
|
public |
Read and write FASTA and FASTQ files efficiently
|
2024-08-20 |
|
lsabgc
|
public |
lsaBGC-Pan - refined workflow for pan-BGC-omic evolutionary investigations.
|
2024-08-20 |
|
ucsc-pslpairs
|
public |
join paired ends in psl alignments
|
2024-08-20 |
|
savana
|
public |
SAVANA: a somatic structural variant caller for long-read data
|
2024-08-20 |
|
resistify
|
public |
A resistance gene annotation tool
|
2024-08-20 |
|
miniprot-boundary-scorer
|
public |
Miniprot boundary scorer parses introns, starts, stops and exons from miniprot's alignment output and scores them
|
2024-08-20 |
