nawrockie Goto Github PK

16s-typestrain-analysis

Scripts for the analysis of the NCBI Genbank 16S-typestrain dataset

ag1

bio-easel

Perl modules and scripts for interfacing with Sean Eddy's C easel sequence analysis library using Perl's Inline.

cmalign_ifile_fetch

Fetch insert or EL sequences in a cmalign output ifile or EL file.

cmsearch_tblout_deoverlap

Script that removes lower scoring overlaps from cmsearch v1.1x --tblout files.

coded_by2extract_fasta_multi_exon

Perl script for converting a NCBI coded_by string to input for the extract_fasta_multi_exon C program

crw-conversion-tools

Scripts originally written for SSU-ALIGN 0.1 development for extracting sequence and structural information from Comparative RNA Website (CRW) file formats.

dnaorg-build-directories

Directories with viral refseq model files to use with the dnaorg scripts.

dnaorg_classify_genomes.pl

Script for classifying genomes based on comparing their annotations. Based on earlier dnaorg_compare_genomes.pl.

dnaorg_compare_genomes

dnaorg_error_code_documentation

Documentation for the error codes used in the dnaorg project, initially developed for viral genome sequence annotation.

dnaorg_fetch_dna_wrapper

dnaorg_install_script

Instructions for a local install of most of the dependencies for the dnaorg scripts. Originally developed for Sergey Zhdanov.

dnaorg_parse_ftable

dnaorg_virus_report

Generate a report about viral sequences given output from dnaorg_virus_wrapper.pl.

dnaorg_virus_wrapper

A wrapper script for comparing viral genomes.

docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

easel-miniapps-documentation

epn-ofile

Perl module for output file handling

epn-options

Perl module for handling command line options, based on Sean Eddy's esl_getopts module from the Easel C library.

epn-test

Perl module for testing perl scripts or perl-based packages.

esl-epn-translate

Script for translating DNA sequences into protein sequences, similar to esl-translate miniapp in Easel C sequence library, but customized for my purposes.

esl-fetch-cds

Bio:Easel script for fetching CDS from NCBI resources.

esl-randomize-sqfile

A script to randomly partition a sequence file, using easel miniapps, originally written in April 2013.

esl-test-cds-translate-vs-fetch

BioEasel script for validating NCBI CDS sequences by comparing fetched protein sequence to translated sequence.

extract_fasta_multi_exon

C program based on Richa Agarwala's extract_fasta that works for genes with multiple exons.

final-project

infernal_gpipe_tests_specificity

Tests on Rfam/Infernal specificity for expansion of GPIPE's use of Rfam annotations.

infernal_gpipe_tests_ssu_lsu

Scripts and other files for testing how well Infernal/Rfam do at annotating LSU and SSU in archaeal and bacterial genomes, for possible inclusion in NCBI's GPIPE prokaryotic genome annotation pipeline.

infernal_gpipe_tests_upgrade_to_1p1

Tests comparing Rfam 12.0 and Rfam 11.0 and Infernal 1.1 versus Infernal 1.0 to see if NCBI's GPIPE prokaryotic genome annotation pipeline can safely update.