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
  ☆491Updated last month
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆851Updated last year
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆404Updated 2 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆445Updated 11 months ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆421Updated last month
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆746Updated 4 months ago
• bioconvert / bioconvert
  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
  ☆385Updated 5 months ago
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆328Updated 8 months ago
• openvax / pyensembl
  Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
  ☆397Updated 3 months ago
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆521Updated last year
• lmdu / pyfastx
  a python package for fast random access to sequences from plain and gzipped FASTA/Q files
  ☆290Updated 11 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆520Updated 3 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆347Updated 3 weeks ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆677Updated 5 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆557Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆495Updated last month
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆309Updated last year
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆456Updated last year
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆878Updated last week
• ebi-pf-team / interproscan
  Genome-scale protein function classification
  ☆353Updated 3 weeks ago
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆623Updated last year
• primer3-org / primer3
  Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
  ☆272Updated 6 months ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆591Updated last year
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆472Updated 3 weeks ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆531Updated 5 months ago
• shenwei356 / taxonkit
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆451Updated 7 months ago
• 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…
  ☆870Updated 2 weeks ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆396Updated last month
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆428Updated 6 months ago