|
miniasm
|
public |
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
|
2025-03-25 |
|
mafft
|
public |
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
|
2025-03-25 |
|
bwa
|
public |
The BWA read mapper.
|
2025-03-25 |
|
spoa
|
public |
SIMD partial order alignment tool/library
|
2025-03-25 |
|
pyspoa
|
public |
Python binding to spoa library.
|
2025-03-25 |
|
mash
|
public |
Fast sequence distance estimator that uses MinHash
|
2025-03-25 |
|
capnproto
|
public |
An insanely fast data interchange format and capability-based RPC system.
|
2025-03-25 |
|
trnascan-se
|
public |
tRNA detection in large-scale genomic sequences
|
2025-03-25 |
|
infernal
|
public |
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
|
2025-03-25 |
|
diamond
|
public |
Accelerated BLAST compatible local sequence aligner
|
2025-03-25 |
|
blast
|
public |
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
|
2025-03-25 |
|
pychopper
|
public |
A tool to identify, orient and rescue full length cDNA reads from nanopore data.
|
2025-03-25 |
|
rasusa
|
public |
Randomly subsample sequencing reads to a specified coverage
|
2025-03-25 |
|
mbtools
|
public |
mbtools - toolkit for working with modification BAM files
|
2025-03-25 |
|
mappy
|
public |
Minimap2 Python binding
|
2025-03-25 |
|
pore-c-py
|
public |
Python scripts for working with Pore-C data
|
2025-03-25 |
|
entrez-direct
|
public |
Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
|
2025-03-25 |
|
epi2melabs
|
public |
Helper library for miscellaneous EPI2ME Labs functionality
|
2025-03-25 |
|
ezcharts
|
public |
eCharts plotting API
|
2025-03-25 |
|
taxonkit
|
public |
A Cross-platform and Efficient NCBI Taxonomy Toolkit
|
2025-03-25 |
|
bracken
|
public |
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
|
2025-03-25 |
|
bedtools
|
public |
A powerful toolset for genome arithmetic
|
2025-03-25 |
|
kraken2
|
public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
|
2025-03-25 |
|
aplanat
|
public |
Bokeh plotting API, with bio-focussed extras.
|
2025-03-25 |
|
sigfig
|
public |
Python library for rounding numbers (with expected results)
|
2025-03-25 |
|
kraken2-server
|
public |
Server implementation of kraken2
|
2025-03-25 |
|
stringtie
|
public |
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
|
2025-03-25 |
|
modbam2bed
|
public |
Summarise BAM files containing modified-base information to bedMethyl format.
|
2025-03-25 |
|
fastcat
|
public |
Concatenate fast/a/q/gz and calculate basic statistics
|
2025-03-25 |
|
gffcompare
|
public |
GffCompare by Geo Pertea
|
2025-03-25 |
|
bcftools
|
public |
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
|
2025-03-25 |
|
libsass
|
public |
A straightforward binding of libsass for Python. Compile Sass/SCSS in Python with no Ruby stack at all!
|
2025-03-25 |
|
flye
|
public |
Fast and accurate de novo assembler for single molecule sequencing reads
|
2025-03-25 |
|
seqkit
|
public |
a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
|
2025-03-25 |
|
minimap2
|
public |
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
|
2025-03-25 |
|
samtools
|
public |
Tools for dealing with SAM, BAM and CRAM files
|
2025-03-25 |
|
htslib
|
public |
C library for high-throughput sequencing data formats.
|
2025-03-25 |
|
pysam
|
public |
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
|
2025-03-25 |
