JamieCFreeman

JamieCFreeman's Stars

• brentp/mosdepth

  fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

  Language:Nim73121219100

• fritzsedlazeck/Sniffles

  Structural variation caller using third generation sequencing

  Language:Python5842751696

• YinLiLin/CMplot

  📊 Circular and Rectangular Manhattan Plot

  Language:R55915137115

• agshumate/Liftoff

  An accurate GFF3/GTF lift over pipeline

  Language:Python475716256

• oushujun/EDTA

  Extensive de-novo TE Annotator

  Language:Perl372953678

• philres/ngmlr

  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

  Language:C++2972210040

• tjiangHIT/cuteSV

  Long read based human genomic structural variation detection with cuteSV

  Language:Python258613037

• wdecoster/nanofilt

  Filtering and trimming of long read sequencing data

  Language:Python20195814

• pjedge/longshot

  diploid SNV caller for error-prone reads

  Language:Rust19959526

• PASApipeline/PASApipeline

  PASA software

  Language:Perl1851231857

• eldariont/svim

  Structural Variant Identification Method using Long Reads

  Language:Python16857420

• timkahlke/LongRead_tutorials

  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data

  13661030

• nanoporetech/pipeline-structural-variation

  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

  Language:Python114272217

• sujaikumar/assemblage

  Tools for working with second gen assemblies, fasta sequences, etc

  Language:Perl9315337

• JustinChu/JupiterPlot

  A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.

  Language:Perl7854611

• clemgoub/dnaPipeTE

  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

  Language:Dockerfile5458611

• wdecoster/nano-snakemake

  A snakemake pipeline for SV analysis from nanopore genome sequencing

  Language:Python5161311

• jbelyeu/SV-plaudit

  Pipeline for structural variant image curation and analysis.

  Language:Shell486242

• cboursnell/crb-blast

  Conditional Reciprocal Best Blast

  Language:Ruby4261011

• darwintreeoflife/darwintreeoflife.data

  Interim data for the Darwin Tree of Life Project

  32727

• mkirsche/Iris

  A module for improving the insertion sequences of structural variant calls

  Language:Java30195

• eswlab/orphan-prediction

  methods for orphan gene prediction paper optimization

  Language:Shell256611

• esolares/HapSolo

  Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding

  Language:Python193106

• TGatter/LazyB

  Economic Genome Assembly from Low Coverage Illumina and Nanopore Data

  Language:Python19140

• guillemylla/Crickets_Genome_Annotation

  Gennome annotation scripts for the crickets Gryllus bimaculatus and Laupala kohalensis.

  Language:HTML13213

• Adamtaranto/blast-besties

  Rapid discovery of reciprocal best blast pairs.

  Language:Python10411

• ConesaLab/MirCure

  microRNA quality control, filter, and curation.

  Language:R5200

• macmanes-lab/orp_website

  Website for Oyster River Protocol

  3211

• rmclarklab/BSA

  Language:Python2102

• CGSbioinfo/RnaSeq

  Language:R1300