josephryan/RyanLabUnixBestPractices

Stars
2
Language
License
GNU General Publi...
Created almost 6 years ago
Updated almost 6 years ago

josephryan/RyanLabUnixBestPractices

josephryan

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

A set of conventions we use in our lab

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

alien_index

identify potential non-animal transcripts in animal transcriptomes

sowhat

Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)

FastqSifter

Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)

phylotocol

template, example, and instructions on how to make an a priori phylogenetic protocol

Hernandez_Ryan_2021_Recoding

Simulation study of recoding effectiveness

leapfrog

identify BLAST hits between two datasets by employing a third intermediate dataset

isoblat

use RNA transcripts to assess assembly - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % mapped, 2) average %coverage of a mapping, and 3) number of transcripts mapping to a single contig/scaffold. It is simple to run. Just run the blat (transcripts vs. genome) and then run the script with the blat-output and your transcript-fasta-file as arguments.

2017-DEEPC_Ctenophora

matemaker

make artificial mate pairs from long sequences for scaffolding

exoblast

compare genome assemblies using sequence similarity to transcript or protein sequences from a different species.

SeaCucumberPhylogenomics

Sea cucumber phylogenomics

hmm2aln.pl

script to automate gene family phylogeny based using HMM

2018-Pastrana_etal_SpongeParaHoxAnalyses

files related to testing for existance of sponge ParaHox genes

Beroe_genome

ctenophore_innexins

Analyses of the innexins of ctenophores

check_for_gold_in_short_seqs

Often before finalizing genome assemblies, short seqs are removed. This script uses transcripts to find bits missing in the long but present in the short. Note:GenBank requires removal of seqs shorter than 200.

2019-DeBiasse_etal_CorellaGenome

Corella genome project scripts, phylotocol, etc.

tmppolar

temporary staging area for polar workshop update

2017b_Sasson_and_Ryan

A reconstruction of sexual modes throughout animal evolution

2018-Hernandez_and_Ryan_HGT

files associated w 2017 HGT study by Hernandez and Ryan

Steinworth_CnidarianHox

Cnidarian Hox Phylotocol and scripts

pal2nal_gblocker

produce a nucleotide alignment that corresponds with a GBLOCKED amino-acid alignment

Ohdera_et_al_2018

3 Acraspeda genomes

RyanLabShortReadAssembly

Our pipeline for assembling short reads

DeBiasse_cnidophylogenomics

phyloconverge

an algorithm to look for convergent signals in phylogenetic trees

make_subalignment

This script takes a prefix of a subset of (our ingroup) taxa and will return an alignment of only those genes within the clade descended from the most recent common ancestor of all genes with the specified prefix.

2017-Kayal_et_al

SELECTINGS

A pipeline to detect positive Darwinian selection in large datasets