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2016-01-21-training-prep

bioconda-recipes

Conda recipes for the bioconda channel.

blast-besties

Rapid discovery of reciprocal best blast pairs.

catcount

Concatenate count tables for RNA-seq reads mapped to features by htseq-count

corset-tools

Companion scripts for annotation of Corset generated transcript clusters.

density-mapr

An R workflow for creating heat-maps representing the spatial association between two genomic feature sets

derip2

Predict progenitor sequence of fungal repeat families by correcting for RIP-like mutations and cytosine deamination events. Mask RIP or deamination events from alignments.

flo

Transfer annotations between genome assemblies using chained whole-genome alignment and UCSC LiftOver. Forked from wurmlab/flo.

frisk

Screen genomic scaffolds for regions of unusual k-mer composition.

gi2descript

Fetch summary data from NCBI for genbank records using GI numbers

graphtagger

Small script to compute coverage of contigs from reads

graphunzip

Unzip assembly graphs with Hi-C data and/or long reads.

hmmlearn

Hidden Markov Models in Python, with scikit-learn like API

howtoscience

A knowledge engine for new students of bioinformatics.

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

low-mem-genomics

Low memory methods for genomic software development

ltr-harvest-reformat

Correct sequence names in LTR_Harvest GFF3 output.

methfreq

Calculate observed vs expected instances of DNA-methylation motifs in gene sequences

mimeo

Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.

mite_hunter_2

Minor edits to allow MITE_Hunter (Han & Wessler 2010) to use modern blast+

mitofinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

mpg

Markovian sequence generator

mpgap

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

nbgrader-gitpod-template

Config scripts for managing nbgrader envs in Gitpod

nearestfeat

Fork of nearestfeat, a tool for calculating distance between members of feature classes in a GFF annotation. Migrating to Python3

planets

Example git repo for wehi git intro course.

promer2circos

Takes promer sequence matches formatted with show_coords, and reformats for use as a circos linkage track

pymummer

Python3 module for running MUMmer and reading the output

quick-ortho-fetch

Take an XML formatted multiblast result, extract genbank IDs for best x hits to each query and download a non-redundant list of matching seqs from ncbi.

reconcile

Take clustered element fragment coordinates from RECON and write sequences to fasta for alignment and consensus calling.