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y-lammers's Projects

abundance_filter icon abundance_filter

Filter sequence data (FASTQ/FASTA) based on abundance. The quality scores of FASTQ data is normalized.

add_taxonomy icon add_taxonomy

Add taxonomic tree information to BLAST hits. Taxonomic information is pulled from the NCBI taxon database.

blast_wrapper icon 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 icon cd-hit-filter

Script for filtering the cluster created by CD-HIT based on the minimum number of reads per cluster.

cites-checker icon cites-checker

Pipeline for BLAST analysis of IonTorrent DNA barcoding data

expand_blast icon 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).

find_snps icon find_snps

Compare two sets of mapping assemblies and return a list of SNPs (or InDels) that can distinguish the two sets.

mergeandfilter icon mergeandfilter

R script for merging and filtering metabarcode data produced by OBITools

metabarcodingfilter icon metabarcodingfilter

Additional metabarcoding filters to correct for tag switching and polymerase biases

obitoolspipeline icon obitoolspipeline

Scripts that run the OBITools pipeline and associated scripts on the cluster

resize_nonchimera icon resize_nonchimera

Duplicate the uchime output so that the output is compatible with the cluster and BLAST script.

split_on_primer icon split_on_primer

Split a FASTQ or FASTA file into sub files based on the primers used.

split_sequence icon split_sequence

Split a sequence file into sub files based on the tags or primers used

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