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

soapdenovo-trans 1.0.5
SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt t...
2 versions - Latest release: about 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
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
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
roary 3.13.0
Rapid large-scale prokaryote pan genome analysis
1 version - Latest release: over 1 year ago - 254 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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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-pyfastaq 3.17.0
Manipulate FASTA and FASTQ files.
7 versions - Latest release: 3 months ago - 1 dependent package - 64 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
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: 5 months ago - 1 dependent package - 1,391 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
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
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
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
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
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
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
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
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
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 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
redundans 0.13c
Redundans pipeline assists an assembly of heterozygous genomes.
2 versions - Latest release: about 2 years ago - 99 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: 3 months ago - 24 dependent packages - 674 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
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-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
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
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 9.9% 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-dnaio 1.2.0
Read and write FASTQ and FASTA
5 versions - Latest release: about 1 month ago - 1 dependent package - 32 stars on GitHub - 1 maintainer
smof 2.13.1
Explore and analyze biological sequence data
1 version - Latest release: about 2 years ago - 12 stars on GitHub
Related Keywords
genomics 19 sequencing 9 pipeline 7 ngs 7 metagenomics 6 sequence-alignment 5 workflow-engine 5 python 5 dna 5 workflow 5 usegalaxy 5 science 5 sequence-analysis 5 hacktoberfest 5 fasta 4 next-generation-sequencing 4 alignment 3 assembly 3 taxonomy 3 fastq 3 microbiome 3 clustering 2 denovo-assembly 2 genome-assembly 2 metabarcoding 2 sequence 2 soapdenovo 2 cpp 2 biology 2 bacteria 2 vcf 2 htslib 2 profile-search 2 computational-biology 2 sequence-search 2 microbiology 2 indels 2 illumina 2 bioinformatics-pipeline 2 global-health 2 infectious-diseases 2 pathogen 2 research 2 umi 1 annotation 1 rust 1 library-complexity 1 sequencing-coverage 1 assembled-contigs 1 closing 1 contigs 1 docker-image 1 gap 1 heterozygous 1 mate-pairs 1 paired-end 1 polymorphic 1 scaffolding 1 bam 1 bcf 1 cram 1 sam 1 fastq-files 1 trimming 1 splitting 1 quality-control 1 quality 1 qc 1 preprocessing 1 polyg 1 overlap 1 merging 1 filtering 1 filter 1 duplication 1 adapter 1 population-genetics 1 python-toolkit 1 species-assignments 1 phylogenetics 1 nomenclature 1 archaea 1 plasmids 1 microbial-genomics 1 metagenome-assembled-genomes 1 mag 1 genome-annotation 1 bacterial-genomes 1 cython 1 bayesian-classifiers 1 16s 1 sequence-clustering 1 mmseqs 1 linclust 1 blast 1 succinct 1 data-structures 1 snvs 1 snps 1 structural-variations 1