Martin Pollard's repositories
agp_tools
Set of tools for working with scaffolds and AGP files
npg_tracking
WTSI Illumina sequencing instruments (HiSeq, MiSeq, GA) tracking
pb-assembly
PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
Scaff10X
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
hla_db_util
Utilities for making sense of the IMGT/HLA database
FALCON_unzip
Making diploid assembly becomes common practice for genomic study
pypop
Python for Population Genomics
synergy-scheduler-manager
Provide advanced scheduling capability for OpenStack using a fairshare algorithm. This is a manager for synergy-service.
blasr
BLASR: The PacBio® long read aligner
m3-avionics
Martlet 3 Avionics
hts-specs
MP15's working changes to the specifications of SAM/BAM and related high-throughput sequencing file formats
pbccs
PacBio circular consensus sequencing
af_analysis
Analysis scripts for 30x vs 15x HiSeq X WGS analysis
hiseq_x_variant_evaluation
Paper in preparation for work on evaluating calling on the Illumina HiSeq X
ggtree
a phylogenetic :palm_tree: viewer for different types of :evergreen_tree: annotations
auto_qc_mkII
Prototype for a non-VRPipe way of running auto-ac
seq_autoqc
Additional high-throughput sequencing autoQC steps
server
A reference implementation of the APIs defined in the schemas repository.
samtools_dev_env
Xcode dev environment for samtools
picard
A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.
htsjdk
Private working repo for htsjdk
zlib
Set up to contribute patches to intel's modifications to zlib
tsv2bin
Sanger SNP DB TSV to Hapmap and VCF converter
pb_calibration
Filter and calibration programs for Illumina BAM files
vr-codebase
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute