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
Top 4.1% on spack.io
20 versions - Latest release: 3 months ago - 24 dependent packages - 674 stars on GitHub - 1 maintainer
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
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
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
Top 10.0% on spack.io
6 versions - Latest release: about 2 years ago - 323 stars on GitHub
manta 1.6.0 removed
Structural variant and indel caller for mapped sequencing data6 versions - Latest release: about 2 years ago - 323 stars on GitHub
Top 9.8% on spack.io
6 versions - Latest release: 5 months ago - 1 dependent package - 1,391 stars on GitHub - 1 maintainer
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
py-dnaio 1.2.0
Read and write FASTQ and FASTA5 versions - Latest release: about 1 month ago - 1 dependent package - 32 stars on GitHub - 1 maintainer
Top 3.7% on spack.io
4 versions - Latest release: about 2 years ago - 14 dependent packages - 1,260 stars on GitHub
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
Top 7.7% on spack.io
4 versions - Latest release: over 1 year ago - 5 dependent packages - 556 stars on GitHub - 1 maintainer
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
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 7.8% on spack.io
4 versions - Latest release: 10 months ago - 2 dependent packages - 1,115 stars on GitHub
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
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
Top 9.9% on spack.io
3 versions - Latest release: 10 months ago - 1 dependent package - 1,450 stars on GitHub
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
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
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
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
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
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
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
redundans 0.13c
Redundans pipeline assists an assembly of heterozygous genomes.2 versions - Latest release: about 2 years ago - 99 stars on GitHub
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
fermikit 2017-11-7
De novo assembly based variant calling pipeline for Illumina short reads1 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 9.6% on spack.io
1 version - Latest release: over 1 year ago - 1 dependent package - 1,077 stars on GitHub - 1 maintainer
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
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
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
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
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
py-cyvcf2 0.11.7 💰
fast vcf parsing with cython + htslib1 version - Latest release: about 2 years ago - 2 dependent packages - 321 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
roary 3.13.0
Rapid large-scale prokaryote pan genome analysis1 version - Latest release: over 1 year ago - 254 stars on GitHub
Top 7.4% on spack.io
1 version - Latest release: over 1 year ago - 2 dependent packages - 1,077 stars on GitHub - 1 maintainer
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
1 version - Latest release: over 1 year ago - 5 dependent packages - 1,077 stars on GitHub - 1 maintainer
py-galaxy-util 22.1.2
Galaxy Generic Utilities1 version - Latest release: over 1 year ago - 5 dependent packages - 1,077 stars on GitHub - 1 maintainer
Top 9.6% on spack.io
1 version - Latest release: over 1 year ago - 1 dependent package - 1,077 stars on GitHub - 1 maintainer
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
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
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
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
smof 2.13.1
Explore and analyze biological sequence data1 version - Latest release: about 2 years ago - 12 stars on GitHub
py-bakta 1.5.1
Bakta: rapid & standardized annotation of bacterial genomes, MAGs & plasmids1 version - Latest release: over 1 year ago - 282 stars on GitHub - 1 maintainer
Top 9.6% on spack.io
1 version - Latest release: over 1 year ago - 1 dependent package - 1,077 stars on GitHub - 1 maintainer
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
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) model1 version - Latest release: about 2 years ago - 125 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
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-ncbi-genome-download 0.3.1
Scripts to download genomes from the NCBI FTP servers1 version - Latest release: over 1 year ago - 730 stars on GitHub - 1 maintainer
Related Keywords
genomics
19
sequencing
9
ngs
7
pipeline
7
metagenomics
6
sequence-alignment
5
dna
5
python
5
workflow
5
hacktoberfest
5
science
5
workflow-engine
5
sequence-analysis
5
usegalaxy
5
next-generation-sequencing
4
fasta
4
fastq
3
microbiome
3
assembly
3
taxonomy
3
alignment
3
bacteria
2
sequence-search
2
biology
2
sequence
2
profile-search
2
illumina
2
genome-assembly
2
soapdenovo
2
computational-biology
2
cpp
2
bioinformatics-pipeline
2
metabarcoding
2
clustering
2
microbiology
2
denovo-assembly
2
research
2
pathogen
2
infectious-diseases
2
global-health
2
htslib
2
indels
2
vcf
2
heterozygous
1
mate-pairs
1
cython
1
paired-end
1
ngs-pipeline
1
methylation-extraction
1
polymorphic
1
methylation
1
bisulfite
1
scaffolding
1
variant-calling
1
ncbi
1
genbank
1
download-genomes
1
command-line
1
bigwig
1
bigbed
1
taxonomic-classification
1
population-genetics
1
python-toolkit
1
plasmids
1
microbial-genomics
1
metagenome-assembled-genomes
1
mag
1
genome-annotation
1
bacterial-genomes
1
annotation
1
rust
1
fastq-files
1
bayesian-classifiers
1
16s
1
viterbi
1
simd
1
protein-structure
1
profile-profile-search
1
opensource
1
hhsearch
1
hhpred
1
hhblits
1
hh-suite
1
gap
1
polyg
1
overlap
1
merging
1
filtering
1
filter
1
duplication
1
adapter
1
species-assignments
1
phylogenetics
1
nomenclature
1
archaea
1
crispr
1
search
1
chimera
1
amplicon
1
fm-index
1