Reverse Dependencies of pysam
The following projects have a declared dependency on pysam:
- CrossMap — CrossMap -- Lift over genomics coordinates between assemblies.
- cstag-cli — Command line interface of cstag to manipulate the minimap2's CS tag
- culebrONT — CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple
- cuteFC — Regenotyping structural variants through an accurate and efficient force-calling method
- cuteSV — Long-read-based human genomic structural variation detection with cuteSV
- cvmtrans — Transposon data process
- cwas — Category-wide association study (CWAS). This is a data analytic tool to perform stringent association tests to find non-coding loci associated with autism spectrum disorder (ASD).
- cyrius — WGS-based CYP2D6 caller
- DAJIN2 — One-step genotyping tools for targeted long-read sequencing
- dcicpyvcf — Variant Call Format (VCF) parser for Python
- Dcon — A program to assess DNA contamination level
- debarcer — A package for de-barcoding and error correction of sequencing data containing molecular barcodes.
- deepaclive — Detecting novel pathogens from NGS reads in real-time during a sequencing run.
- deepconsensus — DeepConsensus
- DeepSomaticCopy — Copy number calling on single cell DNA sequencing data
- deepTools — Useful tools for exploring deep sequencing data.
- DeFCoM — A supervised learning genomic footprinter
- Dellingr — Error supression and variant calling pipeline for Illumina sequencing data
- demuxalot — Scalable and reliable demulitplexing for single-cell RNA sequencing.
- detettore — A tool to detect transposable element polymorphisms
- DiscoPlot — DiscoPlot: identify genomic rearrangements, misassemblies and sequencing artefacts in NGS data
- DISPbind — Disorder protein genomic binding analysis toolkit
- dmg-reads — A simple tool to extract damaged reads from BAM files
- dms2dfe — Pipeline to analyse Deep Mutational Scanning (DMS) experiments in terms of Distribution of Fitness Effects (DFE)
- DNBC4-test — DNBC4 scRNA QC
- DNBC4dev — DNBC4 scRNA QC
- dretools — A software package for finding differential RNA editing.
- DRUGseq-tools — Transcriptome Analysis Pipeline for DRUG-seq
- drukbam — Comandline plotting of sort,indexed bam files
- eds-tools — EDSTools: designed to combined variant calls from peaked data with the reference genome. Returns the genomic sequence of the allele most present in the peak.
- EHdnExact — Refines approximate repeat regions identified by ExpansionHunter denovo to exact genomic coordinates
- ephemeris — Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.
- epilogos — Information-theoretic navigation of multi-tissue functional genomic annotations
- Epinano — call variants, compute variants frequencies from bam file and use the frequencies to predict RNA base modifications
- EpinanoPredict — Predict m6A RNA modifications and train models using SVM
- epiout — EpiOut: outlier detection for DNA accesibility data.
- epiVIA — Virial Integration Analysis with epigenetic data
- epivizFileParser — Parse and Query Genomic File Formats.
- epivizFileServer — A python library to interact, explore and compute data directly from genomic files.
- eQTac — The eQTac method.
- eva-vcf-merge — EBI EVA - VCF merge library
- ezancestry — Easily predict and visualize genetic ancestry. Evaluate custom ancestry-informative SNP sets.
- fast5_rekindler — Collates information from BAM and POD5 files and generates FAST5 files for use in legacy tools such as tailfindr.
- fast5mod — Extraction of modified base data from Guppy Fast5 output
- fast5seek — Get paths for fast5 files contained in BAM, SAM, or fastq.
- fasta-checksum-utils — Library and command-line utility for checksumming FASTA files and individual contigs.
- fba — Tools for single-cell feature barcoding analysis
- fdog — Feature-aware Directed OrtholoG search tool
- fgbio-postprocessing — fgbio_postprocessing
- fgpyo — Python bioinformatics and genomics library
- fibertools — A project for handling fiber-seq data.
- filtersam — ('Tools to filter sam o bam files by percent identity or percent of matched sequence',)
- FinaleToolkit — A package and standalone program to process paired-end reads of cfDNA fragment WGS.
- fings — Filters for Next Generation Sequencing
- fixalign — find and fix missed small exons
- flair-brookslab — flair
- flowsaber — A dataflow based workflow framework
- fluas — no summary
- fuc — Frequently used commands in bioinformatics
- funnSV — Fast and effective functional annotation of SVs
- FusionVet — A bioinformatics tool to visualize and evaluate *known* gene fusions
- galaxy-app — Galaxy application (backend)
- galaxy-data — Galaxy datatype framework and datatypes
- galaxy-tool-util — Galaxy tool and tool dependency utilities
- gauchian — WGS-based GBA variant caller
- gdc-readgroups — From a BAM, convert each readgroup to a json/tsv object needed to create a GDC Read Group node.
- genomeview — genomeview
- genomkit — genomkit
- genomvar — Sequence variant analysis in Python
- genotype — genotype provides an automated pipipeline for comparinggenotypes from different assays.
- geo-upload-tool — CLI tool for preparing data submission to Gene Expression Omnibus
- gerenuq — Samfile long-read filtering script.
- get-read-percid — A simple tool to extract references from BAM files and get read statistics
- get-reads-taxonomy — A simple tool to extract reads from a certain taxa from BAM files
- gff3toddbj — Create a DDBJ annotation file from GFF3 and FASTA files
- gi-ape — no summary
- gimmebio.entropy_scores — no summary
- Giraffe-View — Giraffe_View is specially designed to provide a comprehensive assessment of the accuracy of long-read sequencing datasets obtained from both the PacBio and Nanopore platforms.
- govcf — govcf
- granite-suite — granite is a collection of software to call, filter and work with genomic variants.
- GRATIOSA — no summary
- gretel — An algorithm for recovering potential haplotypes from metagenomes
- gumpy — Genetics with Numpy
- gvc4bam — GVC4BAM is a data processing pipeline developed by Genome Wisdom Inc. GVC4FASTQ detects germline and somatic mutations (SNV, InDel, SV) from BAM files.
- gvc4fastq — GVC4FASTQ is a data processing pipeline developed by Genome Wisdom Inc. GVC4FASTQ detects germline and somatic mutations (SNV, InDel, SV) from FASTQ files.
- handygenome — An integrated platform for genome sequencing analysis
- hapi-pyth — Haplotype-Aware Probabilistic model for Indels
- HaplotagLR — Phasing individual long reads using known haplotype information.
- haptools — Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
- HAT-phasing — HAT: Haplotype assembly tool that use both long and short reads to reconstruct haplotypes
- HiCExplorer — Set of programs to process, analyze and visualize Hi-C data
- hicstuff — General purpose stuff to generate and handle Hi-C data in its simplest form.
- hiMoon — Define names haplotypes from data stored in VCF
- himut — himut: single molecule somatic single-base substitution detection using PacBio CCS reads
- hisv — A computational pipeline for structural variation detection from Hi-C data
- hits-x — Updated and modified from Jeff's version.
- hl7v2GenomicsExtractor — Convert vcf/xml files to HL7V2 message
- HTSeq — A framework to process and analyze data from high-throughput sequencing (HTS) assays
- htseq-clip — htseq-clip: a toolset for the analysis of eCLIP/iCLIP datasets
- hydra-genetics — Helper tools for use with hydra-genetics pipelines.