Pinned Repositories
Anastrepha_ludens_genome_assembly
Scripts used to assemble the Anastrepha ludens genome
Anastrepha_obliqua_genome_assembly
Scripts used to assemble the Anastrepha obliqua genome
blobblurb
Creates a tab-delimited summary blurb of BlobTools output.
FastaParser
Extracts records from a fasta based on a list of fasta headers.
FindContaminantsFromBlob
FindDuplicatesFromBUSCO
Identify duplicate contigs or scaffolds from BUSCO search. Contigs or scaffolds are identified as duplicates when they only contain duplicate BUSCOs and their removal does not impact the number of complete BUSCOs.
HiFiAdapterFilt
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
PopulationGenomicPipeline
Commands for performing a population genomic analysis from genome assembly to population genomic data visualization.
seqer
Return .fasta containing records smaller than or larger than desired length.
YACaSSF
Yet Another Contig and Scaffold Stat Finder
sheinasim's Repositories
sheinasim/HiFiAdapterFilt
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
sheinasim/PopulationGenomicPipeline
Commands for performing a population genomic analysis from genome assembly to population genomic data visualization.
sheinasim/FindDuplicatesFromBUSCO
Identify duplicate contigs or scaffolds from BUSCO search. Contigs or scaffolds are identified as duplicates when they only contain duplicate BUSCOs and their removal does not impact the number of complete BUSCOs.
sheinasim/FindContaminantsFromBlob
sheinasim/Anastrepha_ludens_genome_assembly
Scripts used to assemble the Anastrepha ludens genome
sheinasim/Anastrepha_obliqua_genome_assembly
Scripts used to assemble the Anastrepha obliqua genome
sheinasim/FastaParser
Extracts records from a fasta based on a list of fasta headers.
sheinasim/Find_X_or_Z
Use genotype data (biallelic SNP data in .vcf) to identify X or Z-linked scaffolds.
sheinasim/LEP-Map_Pipe
Pipeline for generating a linkage map and supporting files for QTL analysis
sheinasim/WXYandZ_from_genotypes
Identify X/Z and Y/W linked-scaffolds from genotype heterozygosity and read depth data.
sheinasim/YACaSSF
Yet Another Contig and Scaffold Stat Finder
sheinasim/blobblurb
Creates a tab-delimited summary blurb of BlobTools output.
sheinasim/seqer
Return .fasta containing records smaller than or larger than desired length.
sheinasim/Bombus_huntii_genome_assembly
Scripts used to assemble the Bombus huntii genome
sheinasim/Lachesis_assembly_formatter_for_TASSEL
sheinasim/magic8ball
Python script that answers all of life's questions
sheinasim/mvMapper
mvMapper (Multivariate Mapper) is an interactive data exploration tool for multivariate analyses with associated geographic location information.
sheinasim/porExplorer
Visualize your raw Nanopore or PacBio sequences from fastq
sheinasim/sheinasim.github.io
sheinasim/sim_adapter_manuscript
Repository for commands and scripts used in data analysis for a manuscript
sheinasim/uDownWithAGP
Write NCBI .agp file from scaffold fasta
sheinasim/vim_lessons
Play with these text files and hone your vim skills