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Related:
bioinformatics
cli
sequencing
alignment
bam
sequence-analysis
samtools
assembly
biology
rna-seq
|
| Package |
Description |
Version |
|
mummer
☆
formula
|
Genome alignment tool |
|
|
pangene
☆
formula
|
Construct pangenome gene graphs |
|
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perbase
☆
formula
|
Fast and correct perbase BAM/CRAM analysis |
|
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picard-tools
☆
formula
|
Tools for manipulating HTS data and formats |
|
|
polypolish
☆
formula
|
Short-read polishing tool for long-read assemblies |
|
|
primer3
☆
formula
|
Program for designing PCR primers |
|
|
prodigal
☆
formula
|
Microbial gene prediction |
|
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proteinortho
☆
formula
|
Detecting orthologous genes within different species |
|
|
rasusa
☆
formula
|
Randomly subsample sequencing reads or alignments |
|
|
rna-star
☆
formula
|
RNA-seq aligner |
2.7.11b |
|
ropebwt3
☆
formula
|
BWT construction and search |
|
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sambamba
☆
formula
|
Tools for working with SAM/BAM data |
|
|
samtools
☆
formula
|
Tools for manipulating next-generation sequencing data |
|
|
seqan3
☆
formula
|
Modern C++ library for sequence analysis |
11 |
|
seqtk
☆
formula
|
Toolkit for processing sequences in FASTA/Q formats |
|
|
sickle
☆
formula
|
Windowed adaptive trimming for FASTQ files using quality |
|
|
skani
☆
formula
|
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs |
|
|
spades
☆
formula
|
De novo genome sequence assembly |
4.2.0 |
|
sprocket
☆
formula
|
Bioinformatics workflow engine built on the Workflow Description Language (WDL) |
0.19.0 |
|
sratoolkit
☆
formula
|
Data tools for INSDC Sequence Read Archive |
|
|
stringtie
☆
formula
|
Transcript assembly and quantification for RNA-Seq |
|
|
sylph
☆
formula
|
Ultrafast taxonomic profiling and genome querying for metagenomic samples |
|
|
tabixpp
☆
formula
|
C++ wrapper to tabix indexer |
|
|
trimal
☆
formula
|
Automated alignment trimming in large-scale phylogenetic analyses |
|
|
unipro-ugene
☆
cask
|
Free open-source cross-platform bioinformatics software |
53.1 |
|
vcftools
☆
formula
|
Tools for working with VCF files |
|
|
veryfasttree
☆
formula
|
Efficient phylogenetic tree inference for massive taxonomic datasets |
4 |
|
wfa2-lib
☆
formula
|
Wavefront alignment algorithm library v2 |
|