atmaivancevic Goto Github PK

2017

New Year, New me! Let's hope. This is my attempt at being an organised human being.

allbiotc2

Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.

automated_test

testing automated pipeline for cut n run

aws_setup

bam

Reads and manipulates large BAM files

bedtools

A powerful toolset for genome arithmetic.

beesknees

bovbequidintervals

Stores the tab-delimited txt files of the 33 complete BovB interval sets (from all horses)

chipseq-analysis

chuonglab

General purpose scripts

clustering

Picks the best clustering % identity to use for a given organism/species, taking into account (in order of importance): (a) That higher % ids will produce better alignments (so set a minimum % threshold of 70%); (b) that each cluster needs to be 'alignable' (i.e. set the max size of any given cluster to 100 seqs; unless the % id is very high, e.g. => 90%, in which case the sequences are very similar so the max size of any cluster can be raised to, say, 500 seqs, and still produce a good alignment); (c) that we want to used the largest sample size of sequences possible (i.e. the minimum number of unclustered seqs and singletons, provided the first two conditions are satisfied).

consensus

Makes a consensus sequence for each (given) alignment file. Used to make consensus sequences for the Gblocks-imrpoved alignment file for each cluster (in each species), then concatenates all the cluster consensus seqs for that species into one file.

cut-n-run-analysis

elephant-project

Contains the scripts used to convert BAM to BED, generate binary sequences and infer phylogenies.

erv_cancer_enhancers

forgetfulfish

RNA-seq analysis of zebrafish models of Alzheimer's disease

gblocks

Improve alignment with gblocks to generate a better consensus

genotypegvcfs

Use a whole bunch of vcfs from the variantCalling pipeline to produce a monstrous combined gVCF

giggle_databases

Use public datasets to make giggle databases.

github_tips

How to git better

handyslurmscripts

Handy scripts to summarise job stats (memory used, elapsed time, etc) and produce summary plots

hmmer

Post-HMMer filtering of results

howtodocs

Documentation and usage examples for frequently used pipelines and tools.

kallipygos

Single nucleotide polymorphism that gives sheep "beautiful buttocks"

l1-dynamics

Sample code to accompany the L1 evolutionary dynamics across eukaryotes manuscript. Shows how to perform two independent extraction methods: iterative search using LASTZ on genomic data, versus translated nucleotide search of NCBI databases using TBLASTN. Subsequent analyses use programs such as MUSCLE, USEARCH, HMMER, etc.

landscape

Implements persistence landscape calculation for a set of intervals.

lastz

Use LASTZ for various purposes, such as for screening genomes with potential HT candidates.

longread_vntr_analysis

myblast

pipeline_b

Code used to detect horizontal transfer of transposons across species.