Pinned Repositories
2016-01-28-training-prep
allbiotc2
Benchmark pipeline for Structural Variation analyses, funded by the ALLBio
Amali_Pti_Git
git workshop material
Blueskies16
codfish-hook
Say you're a codfish.
Conferences
A list of conference
delly
DELLY: Structural variant discovery by integrated paired-end and split-read analysis
error_correction
PeerJ Error Correction Paper
Flye
De novo assembler for single molecule sequencing reads using repeat graphs
git-novice
Software Carpentry introduction to Git for novices.
AmaliT's Repositories
AmaliT/Conferences
A list of conference
AmaliT/2016-01-28-training-prep
AmaliT/allbiotc2
Benchmark pipeline for Structural Variation analyses, funded by the ALLBio
AmaliT/Amali_Pti_Git
git workshop material
AmaliT/Blueskies16
AmaliT/codfish-hook
Say you're a codfish.
AmaliT/delly
DELLY: Structural variant discovery by integrated paired-end and split-read analysis
AmaliT/error_correction
PeerJ Error Correction Paper
AmaliT/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
AmaliT/git-novice
Software Carpentry introduction to Git for novices.
AmaliT/Kraken_db_install_scripts
Updated Kraken DB install scripts to cope with new-ish NCBI structure
AmaliT/mcclintock
Meta-pipeline to identify transposable element insertions using next generation sequencing data
AmaliT/methods-and-musings
A (growing) collection of information contributed by Genomics Aotearoa members. Semi blog post style bites of content.
AmaliT/nanopolish
Signal-level algorithms for MinION data
AmaliT/ngs_te_mapper
Software for detecting non-reference transposable element insertions from next-generation sequencing data
AmaliT/planets
swc workshop
AmaliT/planets2
going to mars
AmaliT/RetroSeq
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
AmaliT/sandpit
A demonstration repository
AmaliT/Tangram
Fast Structural Variation Detection Toolbox