Pinned Repositories
acc2taxid
Converts Accession ID to taxid
Anacapa
#### Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
AncestralClust
AncestralClust
AncestralClust_manuscript
Data for the AncestralClust manuscript
calculate_pi_MSA
calculates nucleotide diversity (pi) from a multiple sequence alignment fasta file
CRUX_tutorial
10/16/2020 CaleDNA workshop for running CRUX
SARS_CoV_2_wastewater_surveillance
Method for estimating relative proportions of SARS-CoV-2 strains from wastewater samples
taxid2taxonpath
converts taxids to taxonpaths
tronko
A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets
unix_workshop
Unix Tools, Scripting, and Parallel Computing
lpipes's Repositories
lpipes/tronko
A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets
lpipes/AncestralClust
AncestralClust
lpipes/taxid2taxonpath
converts taxids to taxonpaths
lpipes/SARS_CoV_2_wastewater_surveillance
Method for estimating relative proportions of SARS-CoV-2 strains from wastewater samples
lpipes/unix_workshop
Unix Tools, Scripting, and Parallel Computing
lpipes/calculate_pi_MSA
calculates nucleotide diversity (pi) from a multiple sequence alignment fasta file
lpipes/AncestralClust_manuscript
Data for the AncestralClust manuscript
lpipes/acc2taxid
Converts Accession ID to taxid
lpipes/Anacapa
#### Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
lpipes/CRUX_tutorial
10/16/2020 CaleDNA workshop for running CRUX
lpipes/sam2psl
SAM to psl converter
lpipes/IB134L
code used in IB134L
lpipes/simulator
lpipes/simulator_with_error
lpipes/snapi_assessment
lpipes/SPscore
calculates sum-of-pairs score for Multiple Sequence Alignment
lpipes/SQUAT
a Sequencing Quality Assessment Tool