zheludev Goto Github PK

followers: 3.0 following: 1.0 repos: 8.0 gists: 0.0

Name: Zheludev

Type: User

Bio: Stanford biochemistry graduate student working on RNA in the Fire Lab - mostly focusing on strange RNA elements and viruses

Twitter: RZheludev

Blog: https://orcid.org/0000-0002-9572-0574

Zheludev's Projects

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

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