Alternatives and similar repositories for pysam

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

• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆988Updated 4 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,337Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆838Updated 2 months ago
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,010Updated 11 months ago
• mdshw5 / pyfaidx
  Efficient pythonic random access to fasta subsequences
  ☆478Updated 2 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆771Updated last month
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆495Updated this week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆727Updated 7 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆507Updated 8 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆830Updated last year
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆520Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆726Updated 2 weeks ago
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,023Updated last week
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆438Updated last year
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆838Updated last week
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆691Updated last week
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆407Updated 10 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,480Updated 2 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆866Updated 6 months ago
• chapmanb / bcbb
  Incubator for useful bioinformatics code, primarily in Python and R
  ☆626Updated 6 months ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆481Updated 4 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆857Updated 3 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆786Updated 3 weeks ago
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆685Updated 3 weeks ago
• igvteam / igv.js
  Embeddable genomic visualization component based on the Integrative Genomics Viewer
  ☆683Updated this week
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆814Updated last year
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆508Updated last year
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆693Updated 3 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆427Updated 3 months ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆811Updated last week