Zheludev
Stanford biochemistry graduate student working on RNA in the Fire Lab - mostly focusing on strange RNA elements and viruses
Pinned Repositories
fast_hdbscan
A fast multi-core implementation of HDBSCAN for low dimensional Euclidean spaces
Bracken2OTU
simple python script that takes Bracken outputs and merges them into one OTU table, user can specify if a subset of outputs need to be summed together prior to appending to the OTU table
FireTools
a parent repo for tools written by I.N.Z during their tenure at the Fire Lab
KmerCatcher
A simple python script that counts k-mer matches between reference database and query .fasta files, optionally returning all non-matching query sequences. Designed originally for sequencing adapter decontamination.
KrakenGrafter
a simple python script for "grafting" on novel sequences to a custom Kraken2 database
MSAcleaner
a simple python script that takes in a FASTA formatted MSA and, given a set of 'reference' sequences, deletes any sequences that contribute to insertions given a fractional abundance
SeqDoubler
a trivial python script that doubles input FASTA formatted sequences end on - helps deal with bisection due to circular permutation
SeqMatchCheck
a simple bash script based on bioawk that checks if two .fastx files have exactly matching sequences in the same positions - used to check if fastp made a duplication error
VNom
Viroid Nominator (VNom): reference free tool for nominating viroid-like de novo assembled contigs
Zheludev's Repositories
Zheludev/VNom
Viroid Nominator (VNom): reference free tool for nominating viroid-like de novo assembled contigs
Zheludev/KrakenGrafter
a simple python script for "grafting" on novel sequences to a custom Kraken2 database
Zheludev/Bracken2OTU
simple python script that takes Bracken outputs and merges them into one OTU table, user can specify if a subset of outputs need to be summed together prior to appending to the OTU table
Zheludev/FireTools
a parent repo for tools written by I.N.Z during their tenure at the Fire Lab
Zheludev/KmerCatcher
A simple python script that counts k-mer matches between reference database and query .fasta files, optionally returning all non-matching query sequences. Designed originally for sequencing adapter decontamination.
Zheludev/MSAcleaner
a simple python script that takes in a FASTA formatted MSA and, given a set of 'reference' sequences, deletes any sequences that contribute to insertions given a fractional abundance
Zheludev/SeqDoubler
a trivial python script that doubles input FASTA formatted sequences end on - helps deal with bisection due to circular permutation
Zheludev/SeqMatchCheck
a simple bash script based on bioawk that checks if two .fastx files have exactly matching sequences in the same positions - used to check if fastp made a duplication error