Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

spack.io "bioinformatics" keyword

andi 0.14
andi is used for for estimating the evolutionary distance between closely related genomes.
2 versions - Latest release: about 2 years ago - 34 stars on GitHub - 1 maintainer
preseq 2.0.3
The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing l...
2 versions - Latest release: 10 months ago - 60 stars on GitHub
smof 2.13.1
Explore and analyze biological sequence data
1 version - Latest release: about 2 years ago - 12 stars on GitHub
rdptools 2.0.2
Collection of commonly used RDP Tools for easy building.
1 version - Latest release: about 2 years ago - 1 dependent package - 45 stars on GitHub
psmc 2016-1-21
mplementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
1 version - Latest release: about 2 years ago - 125 stars on GitHub
Top 9.6% on spack.io
py-galaxy-job-metrics 22.1.1
The Galaxy job metrics framework and default plugins.
1 version - Latest release: over 1 year ago - 1 dependent package - 1,077 stars on GitHub - 1 maintainer
Top 9.6% on spack.io
py-galaxy-objectstore 22.1.1
The Galaxy object store framework and default implementations.
1 version - Latest release: over 1 year ago - 1 dependent package - 1,077 stars on GitHub - 1 maintainer
Top 9.6% on spack.io
py-galaxy-containers 22.1.1
The Galaxy containers module - interfaces for modeling and interacting with container backends (d...
1 version - Latest release: over 1 year ago - 1 dependent package - 1,077 stars on GitHub - 1 maintainer
Top 5.1% on spack.io
py-galaxy-util 22.1.2
Galaxy Generic Utilities
1 version - Latest release: over 1 year ago - 5 dependent packages - 1,077 stars on GitHub - 1 maintainer
Top 7.4% on spack.io
py-galaxy-tool-util 22.1.5
The Galaxy tool utilities.
1 version - Latest release: over 1 year ago - 2 dependent packages - 1,077 stars on GitHub - 1 maintainer
py-gtdbtk 2.3.2
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and ...
3 versions - Latest release: 8 months ago - 327 stars on GitHub - 1 maintainer
py-piper 0.12.3
A lightweight python toolkit for gluing together restartable, robust shell pipelines.
1 version - Latest release: over 1 year ago - 1 dependent package - 35 stars on GitHub - 1 maintainer
kalign 3.4.0
A fast multiple sequence alignment program for biological sequences.
2 versions - Latest release: 4 months ago - 1 dependent package - 89 stars on GitHub
py-dnaio 1.2.0
Read and write FASTQ and FASTA
5 versions - Latest release: 25 days ago - 1 dependent package - 32 stars on GitHub - 1 maintainer
roary 3.13.0
Rapid large-scale prokaryote pan genome analysis
1 version - Latest release: over 1 year ago - 254 stars on GitHub
libbigwig 0.4.7
A C library for reading/parsing local and remote bigWig and bigBed files.
1 version - Latest release: over 1 year ago - 1 dependent package - 61 stars on GitHub - 1 maintainer
py-cyvcf2 0.11.7 💰
fast vcf parsing with cython + htslib
1 version - Latest release: about 2 years ago - 2 dependent packages - 321 stars on GitHub - 1 maintainer
mmseqs2 13-45111
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge pro...
2 versions - Latest release: over 1 year ago - 2 dependent packages - 900 stars on GitHub
Top 7.7% on spack.io
vsearch 2.22.1
VSEARCH is a versatile open-source tool for metagenomics.
4 versions - Latest release: over 1 year ago - 5 dependent packages - 556 stars on GitHub - 1 maintainer
soapdenovo-trans 1.0.5
SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt t...
2 versions - Latest release: almost 2 years ago - 28 stars on GitHub - 1 maintainer
Top 7.8% on spack.io
seqtk 1.4
Toolkit for processing sequences in FASTA/Q formats.
4 versions - Latest release: 10 months ago - 2 dependent packages - 1,115 stars on GitHub
Top 4.1% on spack.io
htslib 1.19.1
C library for high-throughput sequencing data formats.
20 versions - Latest release: 2 months ago - 24 dependent packages - 674 stars on GitHub - 1 maintainer
sortmerna 2017-07-13
SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomi...
1 version - Latest release: about 2 years ago - 169 stars on GitHub
readfq 2013.04.10
Readfq is a collection of routines for parsing the FASTA/FASTQ format. It seamlessly parses both ...
1 version - Latest release: about 2 years ago - 155 stars on GitHub
py-ncbi-genome-download 0.3.1
Scripts to download genomes from the NCBI FTP servers
1 version - Latest release: over 1 year ago - 730 stars on GitHub - 1 maintainer
fermikit 2017-11-7
De novo assembly based variant calling pipeline for Illumina short reads
1 version - Latest release: about 2 years ago - 105 stars on GitHub
fermi 1.1
A WGS de novo assembler based on the FMD-index for large genomes.
1 version - Latest release: about 2 years ago - 74 stars on GitHub
soapdenovo2 240
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the ...
2 versions - Latest release: about 2 years ago - 189 stars on GitHub - 1 maintainer
py-pispino 1.1
PISPINO (PIpits SPIN-Off tools).
1 version - Latest release: about 2 years ago - 1 dependent package - 2 stars on GitHub - 1 maintainer
methyldackel 0.6.1
MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILE...
1 version - Latest release: over 1 year ago - 126 stars on GitHub - 1 maintainer
fq 0.10.0
fq is a library to generate and validate FASTQ file pairs. fq provides subcommands for filtering,...
1 version - Latest release: 8 months ago - 50 stars on GitHub - 1 maintainer
bioawk 1.0
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological ...
1 version - Latest release: about 2 years ago - 541 stars on GitHub
Top 9.9% on spack.io
fastp 0.23.4
A tool designed to provide fast all-in-one preprocessing for FastQ files.
3 versions - Latest release: 10 months ago - 1 dependent package - 1,450 stars on GitHub
py-bakta 1.5.1
Bakta: rapid & standardized annotation of bacterial genomes, MAGs & plasmids
1 version - Latest release: over 1 year ago - 282 stars on GitHub - 1 maintainer
swarm 3.0.0
A robust and fast clustering method for amplicon-based studies.
2 versions - Latest release: about 2 years ago - 105 stars on GitHub
Top 9.8% on spack.io
minimap2 2.17
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a la...
6 versions - Latest release: 4 months ago - 1 dependent package - 1,391 stars on GitHub - 1 maintainer
hh-suite 3.3.0
HH-suite is a widely used open source software suite for sensitive sequence similarity searches a...
1 version - Latest release: over 1 year ago - 1 dependent package - 420 stars on GitHub
py-pyfastaq 3.17.0
Manipulate FASTA and FASTQ files.
7 versions - Latest release: 3 months ago - 64 stars on GitHub - 1 maintainer
megahit 1.1.4
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succi...
2 versions - Latest release: about 2 years ago - 448 stars on GitHub
kaiju 1.6.2
Kaiju is a program for the taxonomic classification of high-throughput sequencing reads.
1 version - Latest release: about 2 years ago - 212 stars on GitHub
minced 0.4.2
MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) i...
4 versions - Latest release: over 1 year ago - 1 dependent package - 81 stars on GitHub
Top 3.7% on spack.io
bwa 0.7.17
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
4 versions - Latest release: about 2 years ago - 14 dependent packages - 1,260 stars on GitHub
wgsim 2011.10.17
Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simula...
1 version - Latest release: about 2 years ago - 228 stars on GitHub
py-drep 3.4.2
dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replic...
2 versions - Latest release: about 1 year ago - 172 stars on GitHub - 1 maintainer
redundans 0.13c
Redundans pipeline assists an assembly of heterozygous genomes.
2 versions - Latest release: about 2 years ago - 99 stars on GitHub
strelka 2.9.10 removed
Somatic and germline small variant caller for mapped sequencing data.
14 versions - Latest release: about 2 years ago - 293 stars on GitHub
Top 10.0% on spack.io
manta 1.6.0 removed
Structural variant and indel caller for mapped sequencing data
6 versions - Latest release: about 2 years ago - 323 stars on GitHub
Related Keywords
genomics 19 sequencing 9 ngs 7 pipeline 7 metagenomics 6 dna 5 sequence-alignment 5 hacktoberfest 5 science 5 sequence-analysis 5 usegalaxy 5 workflow 5 workflow-engine 5 python 5 fasta 4 next-generation-sequencing 4 fastq 3 taxonomy 3 microbiome 3 alignment 3 assembly 3 pathogen 2 research 2 genome-assembly 2 sequence-search 2 htslib 2 vcf 2 infectious-diseases 2 global-health 2 profile-search 2 bioinformatics-pipeline 2 denovo-assembly 2 cpp 2 soapdenovo 2 indels 2 biology 2 sequence 2 computational-biology 2 microbiology 2 metabarcoding 2 bacteria 2 illumina 2 clustering 2 hhpred 1 hhblits 1 spliced-alignment 1 hh-suite 1 hhsearch 1 structural-variations 1 plasmids 1 microbial-genomics 1 metagenome-assembled-genomes 1 mag 1 genome-annotation 1 bacterial-genomes 1 annotation 1 umi 1 trimming 1 splitting 1 quality-control 1 quality 1 qc 1 preprocessing 1 polyg 1 structural-variation 1 snvs 1 snps 1 scaffolding 1 polymorphic 1 paired-end 1 mate-pairs 1 heterozygous 1 gap 1 docker-image 1 contigs 1 closing 1 assembled-contigs 1 microbial-genomes 1 fm-index 1 crispr 1 taxonomic-classification 1 succinct 1 data-structures 1 viterbi 1 simd 1 protein-structure 1 profile-profile-search 1 opensource 1 search 1 chimera 1 amplicon 1 sequence-clustering 1 mmseqs 1 linclust 1 blast 1 cython 1 bigwig 1 bigbed 1 python-toolkit 1 species-assignments 1