Antigenic Cartography's repositories
figtree-recolor
A script to re-color a FigTree saved Nexus file
2018-cambridge-python-course
Notes and code from a May 2018 course on Python and the shell
acmacs-chart-1
Accessing chart data (acmacs-d)
antigenic-map-viewer
Antigenic Map Viewer for 3D and 2D maps. To be embedded into AcmacsWeb.
christian-beast
Convert taxa and their feature values from CSV to XML for BEAST
compare-metagenomics-benchmark-pipeline-spec
A SLURM pipeline specification file and associated scripts for processing a set of reads for a COMPARE metagenomics benchmark.
condor-ansible
Ansible playbooks for managing the condor cluster machines
eske-baikal-initial-spec
A slurm-pipeline specification and scripts for processing Eske Baikal data
eske-blastn-pipeline-spec
blastn SLURM pipeline specification and scripts for processing Eske Willerslev ancient DNA
eske-bronze-initial-spec
A slurm-pipeline specification and scripts for processing Eske bronze age data
eske-diamond-panel-redo
A SLURM pipeline re-do of the noninteractive alignment panel processing, with reads grouped by subject
eske-pipeline-spec
A slurm-pipeline specification and scripts for processing Eske data
greedy-lib
Python library for running greedy selection of model parameters
lasse-capture-20180425-bwa-hbv
SLURM pipeline spec for processing Lasse 2018-04-25 capture data using bwa
lasse-capture-20180425-hbv-collector
SLURM pipeline spec for collecting Lasse 2018-04-25 capture HBV data
neo-hbv-collector-pipeline
A pipeline for collecting HBV results from other pipelines
neo-pipeline
SLURM pipeline for processing neo aDNA samples
puffinosis-diamond-bacterial
A slurm-pipeline specification and scripts for running Puffinosis reads against the NCBI bacterial refseq
puffinosis-diamond-viral
A slurm-pipeline specification and scripts for running Puffinosis reads against the NCBI viral refseq
seqdb-make-tree-signature-page
Set of tools to build, query sequence database and to generate phylogenetic trees.
sofia-blastx-pipeline
A slurm-pipeline specification and scripts for processing Sofia data
sofia-pipeline
A pipeline for Sofia P
wendy-changes
Code to find nucleotide and aa changes in a FASTA file
whocc-sequences
Set of tools to keep WHO CCs flu sequence database (H1, H3, B) and perform various analysis