Pinned Repositories
alnSeq
AlnSeq runs a c coded Smith Waterman, Needleman Wunsch, and an Hirschberg.
annotateASFV
A collection of bash scripts to allow a reference based annotation of ASFV genomes
artic-reference-benchmark
My goal is to see how the choice of a reference genome affects the artic pipelines accuracy.
assembler-scripts
Scripts I used to run assemblers for the 2021 benchmarking study
bioTools
a series small, niche biiology tools. These are not overall very usefull, except to me.
find--Co-infections
A pipeline to detect co-infections from Nanopore reads.
fluDI
Find complete diRNA and vRNA influenza reads ids in long reads. Use something like fqGetIds or seqkit to extract reads by read ids.
getHaPath
Checks to see if a flu HA sequence belongs to a high path or low path flu strain.
nbib-to-bib
Converts a nbib file to a bibtex file
pandoc-ditaa
Pandoc-ditaa is a pandoc lua filter that used ditaa to convert ascii digrams in markdown files into images.
jeremyButtler's Repositories
jeremyButtler/find--Co-infections
A pipeline to detect co-infections from Nanopore reads.
jeremyButtler/nbib-to-bib
Converts a nbib file to a bibtex file
jeremyButtler/alnSeq
AlnSeq runs a c coded Smith Waterman, Needleman Wunsch, and an Hirschberg.
jeremyButtler/annotateASFV
A collection of bash scripts to allow a reference based annotation of ASFV genomes
jeremyButtler/artic-reference-benchmark
My goal is to see how the choice of a reference genome affects the artic pipelines accuracy.
jeremyButtler/assembler-scripts
Scripts I used to run assemblers for the 2021 benchmarking study
jeremyButtler/bioTools
a series small, niche biiology tools. These are not overall very usefull, except to me.
jeremyButtler/fluDI
Find complete diRNA and vRNA influenza reads ids in long reads. Use something like fqGetIds or seqkit to extract reads by read ids.
jeremyButtler/fqGetIds
A program using SMID vectors to extract fastq reads by read ids.
jeremyButtler/getHaPath
Checks to see if a flu HA sequence belongs to a high path or low path flu strain.
jeremyButtler/Nano-Q--wrapper
This is a wrapper to run PrestonLeung's Nano-Q with
jeremyButtler/pandoc-ditaa
Pandoc-ditaa is a pandoc lua filter that used ditaa to convert ascii digrams in markdown files into images.
jeremyButtler/who2023-TB-catalog-as-tsv
My attempt to convert the WHO's second addition TB catalog to a flat file