robsyme/fasta_util

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1
Language
Ruby
License
MIT License
Created almost 14 years ago
Updated about 13 years ago

robsyme/fasta_util

robsyme

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An easy way of performing some common operations on fasta files

nextflow-annotate

Workflows I find helpful for fungal genome annotation

nf-repeatmasking

Nextflow workflow for automatic repeat detection, classification and masking

succinctBitSet

Fast rank and select operations on indexed bitsets.

obo

A parser for the OBO flat file format

nf-annotate

Fungal genome annotation pipeline

robsyme.com

Source for personal site

wavelettree

Rough sketches of wavelet trees for providing fast rank queries on non-binary alphabets.

mitehunter

A clone of MITE-Hunter from Yujun Han and Susan Wessler - used for bugfixing

bioruby-chado

A library that allows you to pull ruby objects out of a Chado-schema database

workflows-proteogenomics

Versioned, shareable and replicable workflows for proteogenomics.

cegma-docker

Docker container for running CEGMA

polymer-region-selector

A widget that selects max and min bounds on a genomic sequence of a given length.

gortex

Tool to pull out species-specific sequence from coloured graphs generated by Cortex-var

docker-REPET

The REPET package in a container.

nf-test

A repository for various tests and minimal-reproducible-example workflows

nf-cid

A Nextflow plugin for interacting with content-addressed data.

GeneMark-Extractor

Tools for taking GeneMark output and pulling out the relevant sequences from the original fasta file.

busco

https://gitlab.com/ezlab/busco

acnfp-trans-counter

A very quick and dirty project to help out a colleague

Parastagonospora_nodorum_SN15

Storage and edit history for ACNFP gene models.

bioruby-lazyblastxml

A plugin that allows you to parse large blast XML output files lazily, reading only what you need.

comparative-sketch

A very quick and dirty sketch to quickly visualise large-scale genome comparisons in non-model organisms. Also might be handy for creating SVG drafts which can be cleaned up in Inkscape for publication.

modules

Minimal nf-core style modules repository