Amali Thrimawithana's repositories
Conferences
A list of conference
Amali_Pti_Git
git workshop material
codfish-hook
Say you're a codfish.
error_correction
PeerJ Error Correction Paper
git-novice
Software Carpentry introduction to Git for novices.
Kraken_db_install_scripts
Updated Kraken DB install scripts to cope with new-ish NCBI structure
mcclintock
Meta-pipeline to identify transposable element insertions using next generation sequencing data
methods-and-musings
A (growing) collection of information contributed by Genomics Aotearoa members. Semi blog post style bites of content.
nanopolish
Signal-level algorithms for MinION data
ngs_te_mapper
Software for detecting non-reference transposable element insertions from next-generation sequencing data
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.