Alternatives and similar repositories for pyfaidx

Users that are interested in pyfaidx are comparing it to the libraries listed below

• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆484Updated 6 months ago
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆399Updated 4 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆838Updated last year
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆324Updated 6 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆433Updated 8 months ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆412Updated this week
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated 2 weeks ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆733Updated last month
• lmdu / pyfastx
  a python package for fast random access to sequences from plain and gzipped FASTA/Q files
  ☆288Updated 8 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆339Updated 3 weeks ago
• openvax / pyensembl
  Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
  ☆397Updated last month
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆485Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆510Updated last week
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆459Updated 3 weeks ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆306Updated last year
• bioconvert / bioconvert
  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
  ☆382Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆545Updated last year
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆649Updated 2 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆433Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆451Updated last year
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆511Updated last year
• pysam-developers / pysam
  Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…
  ☆851Updated 3 months ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 3 months ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆584Updated last year
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆608Updated 9 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆520Updated 2 months ago
• pcingola / SnpEff
  ☆290Updated last week
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆476Updated this week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆377Updated 3 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆698Updated 5 months ago