Pinned Repositories
Abundance_Filter
Filter sequence data (FASTQ/FASTA) based on abundance. The quality scores of FASTQ data is normalized.
Add_taxonomy
Add taxonomic tree information to BLAST hits. Taxonomic information is pulled from the NCBI taxon database.
BLAST_wrapper
A wrapper for either running local BLAST searches with the NCBI-BLAST+ tool or online BLAST searches with the Bio-Python module.
CD-HIT-Filter
Script for filtering the cluster created by CD-HIT based on the minimum number of reads per cluster.
Cites-checker
Pipeline for BLAST analysis of IonTorrent DNA barcoding data
Cluster-pipeline
454 sequence clustering and identification
HaplogroupEstimation
Script used for the haplogroup estimation across smaller variant windows.
MergeAndFilter
R script for merging and filtering metabarcode data produced by OBITools
MetabarcodingFilter
Additional metabarcoding filters to correct for tag switching and polymerase biases
Split_on_Primer
Split a FASTQ or FASTA file into sub files based on the primers used.
Y-Lammers's Repositories
Y-Lammers/CD-HIT-Filter
Script for filtering the cluster created by CD-HIT based on the minimum number of reads per cluster.
Y-Lammers/Split_on_Primer
Split a FASTQ or FASTA file into sub files based on the primers used.
Y-Lammers/Add_taxonomy
Add taxonomic tree information to BLAST hits. Taxonomic information is pulled from the NCBI taxon database.
Y-Lammers/MergeAndFilter
R script for merging and filtering metabarcode data produced by OBITools
Y-Lammers/MetabarcodingFilter
Additional metabarcoding filters to correct for tag switching and polymerase biases
Y-Lammers/Abundance_Filter
Filter sequence data (FASTQ/FASTA) based on abundance. The quality scores of FASTQ data is normalized.
Y-Lammers/BLAST_wrapper
A wrapper for either running local BLAST searches with the NCBI-BLAST+ tool or online BLAST searches with the Bio-Python module.
Y-Lammers/Cites-checker
Pipeline for BLAST analysis of IonTorrent DNA barcoding data
Y-Lammers/Cluster-pipeline
454 sequence clustering and identification
Y-Lammers/HaplogroupEstimation
Script used for the haplogroup estimation across smaller variant windows.
Y-Lammers/Compare_BLAST
Compare the results from multiple BLAST runs.
Y-Lammers/Expand_BLAST
Expand the tsv output from either the BLAST_wrapper or HTS-barcode-checker pipeline with the number of reads for each cluster (based on CD-hit clustering).
Y-Lammers/FASTQ_Filter
Small Script to trim and filter FASTQ reads.
Y-Lammers/Find_SNPs
Compare two sets of mapping assemblies and return a list of SNPs (or InDels) that can distinguish the two sets.
Y-Lammers/Metabarcoding_Blacklists
Metabarcoding blacklists
Y-Lammers/OBIToolsPipeline
Scripts that run the OBITools pipeline and associated scripts on the cluster
Y-Lammers/Resize_nonChimera
Duplicate the uchime output so that the output is compatible with the cluster and BLAST script.
Y-Lammers/Split_sequence
Split a sequence file into sub files based on the tags or primers used