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pyvcf3
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public |
A Variant Call Format reader for Python
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2025-03-25 |
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unikmer
|
public |
A versatile toolkit for k-mers with taxonomic information
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2025-03-25 |
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clair3-trio
|
public |
Clair3-Trio is a variants caller tailored for family trios from nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model that allows it to input all trio’s sequencing information and output all trio’s predicted variants within a single model, to perform far better variant calling. We also present MCVLoss, the first loss function that can improve variants calling in trios by leveraging the explicitly encoding of the priors of the Mendelian inheritance in trios. Clair3-Trio showed comprehensive improvement in experiments. It predicted much fewer Mendelian inheritance violation variations than current state-of-the-art methods.
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2025-03-25 |
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cladebreaker
|
public |
Nextflow pipeline for phylogenetic analysis.
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2025-03-25 |
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lisa2
|
public |
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. X. Shirley Liu Lab, 2020
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2025-03-25 |
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chronumental
|
public |
Make time trees from large phylogenetic divergence trees
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2025-03-25 |
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yahs
|
public |
YaHS, yet another Hi-C scaffolding tool.
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2025-03-25 |
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parse_mito_blast
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public |
Filtering blast out from querying assembly against mitochondrial database.
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2025-03-25 |
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pbtk
|
public |
pbtk - PacBio BAM toolkit
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2025-03-25 |
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perl-devel-checklib
|
public |
check that a library is available
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2025-03-25 |
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mgcplotter
|
public |
Microbial Genome Circular plotting tool using Circos
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2025-03-25 |
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genbank_to
|
public |
genbank_to: convert genbank files to a swath of other formats
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2025-03-25 |
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gassst
|
public |
GASSST : Global Alignment Short Sequence Search Tool
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2025-03-25 |
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btllib
|
public |
Bioinformatics common code library in C++ with Python wrappers, from Bioinformatics Technology Lab
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2025-03-25 |
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biosniff
|
public |
A Sniffer for Biological formats
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2025-03-25 |
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astral-tree
|
public |
ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.
|
2025-03-25 |
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gctb
|
public |
GCTB (Genome-wide Complex Trait Bayesian ) is a software tool that comprises a family of Bayesian linear mixed models for complex trait analyses using genome-wide SNPs.
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2025-03-25 |
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aeon
|
public |
Python/Rust library for symbolic manipulation of Boolean networks.
|
2025-03-25 |
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metaplex
|
public |
Read Processing and Quality Control Toolkit for Dual-Indexed Metabarcoding
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2025-03-25 |
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ngslca
|
public |
ngsLCA: fast and flexible taxonomic classification of DNA reads aligned to reference databases
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2025-03-25 |
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hmtnote
|
public |
Human mitochondrial variants annotation using HmtVar.
|
2025-03-25 |
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prscs
|
public |
PRS-CS is a Python based command line tool that infers posterior SNP effect sizes under continuous shrinkage (CS) priors using GWAS summary statistics and an external LD reference panel.
|
2025-03-25 |
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vcfpy2
|
public |
Python 3 VCF library, based on vcfpy.
|
2025-03-25 |
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prot-scriber
|
public |
Assigns short human readable descriptions (HRD) to query biological sequences using reference candidate descriptions.
|
2025-03-25 |
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greenhill
|
public |
A de novo chromosomal-level scaffolding and phasing tool using Hi-C
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2025-03-25 |
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naltorfs
|
public |
Nested Alternate Open Reading Frames (nAlt-ORFs)
|
2025-03-25 |
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scar
|
public |
scAR (single-cell Ambient Remover) is a deep learning model for ambient signal removal in droplet-based single cell omicsis.
|
2025-03-25 |
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aniclustermap
|
public |
A tool for drawing ANI clustermap between all-vs-all microbial genomes
|
2025-03-25 |
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bwa-meme
|
public |
Faster BWA-MEM2 using learned-index
|
2025-03-25 |
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automappa
|
public |
Automappa: An interactive interface for exploration of metagenomes
|
2025-03-25 |
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scelestial
|
public |
Scelestial, Single Cell Lineage Tree Inference based on a Steiner Tree Approximation Algorithm
|
2025-03-25 |
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pyroe
|
public |
A python toolkit to aid with scRNA-seq analysis workflows using alevin-fry
|
2025-03-25 |
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propy3
|
public |
Python library for calculating various protein descriptors from protein sequences
|
2025-03-25 |
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bigscape
|
public |
Biosynthetic Genes Similarity Clustering and Prospecting Engine.
|
2025-03-25 |
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notramp
|
public |
Super-fast Normalization and Trimming for Amplicon Sequencing Data (Long- and Short-read)
|
2025-03-25 |
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cogclassifier
|
public |
Classify prokaryote protein sequences into COG functional category
|
2025-03-25 |
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gbkviz
|
public |
Simple web application to visualize and compare genomes in Genbank files
|
2025-03-25 |
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ampliconclassifier
|
public |
AmpliconClassifier classifies the output of AmpliconArchitect to detect different types of focal amplifications.
|
2025-03-25 |
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perl-alien-build
|
public |
Build external dependencies for use in CPAN
|
2025-03-25 |
|
perl-alien-libxml2
|
public |
Install the C libxml2 library on your system
|
2025-03-25 |
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perl-ffi-checklib
|
public |
Check that a library is available for FFI
|
2025-03-25 |
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poseidon-xerxes
|
public |
A tool (xerxes) to analyse genotype databases formatted using Poseidon.
|
2025-03-25 |
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perl-class-trigger
|
public |
Mixin to add / call inheritable triggers
|
2025-03-25 |
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lmas
|
public |
LMAS - Last (Meta)Genomic Assembler Standing
|
2025-03-25 |
|
pmlst
|
public |
Plasmid Multi-Locus Sequence Typing
|
2025-03-25 |
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pprodigal
|
public |
PProdigal - Parallelized gene prediction based on Prodigal.
|
2025-03-25 |
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metanovo
|
public |
Produce targeted databases for mass spectrometry analysis.
|
2025-03-25 |
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polypolish
|
public |
Polishing genome assemblies with short reads.
|
2025-03-25 |
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perl-bio-searchio-hmmer
|
public |
A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
|
2025-03-25 |
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phykit
|
public |
PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.
|
2025-03-25 |
