samtools

Efficient pythonic random access to fasta subsequences

The ChIP-Seq peak calling algorithm using convolution neural networks

Installation and usage for various tools for cancer genomics

Get sex info from BAM file

Curated cheatsheet of high-efficiency Linux, AWK, SAMtools, BCFtools, SeqKit, and Python one-liners for daily genomic data manipulation.

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

Collecting Genotypes from ENA and make their SNPs

Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog

Take information about snps on short sequence reads and accurately place the snps in a reference genome

A complete workflow for analyzing and visualizing bulk RNA-seq data.

Some NGS library preps use amplicons, and it can be difficult to determine the coverage and depth of each amplicon.

For comparing the subgenomes of wheat

Synthetic somatic mutation read-generation, variant calling pipelines (DeepVariant & GATK), and benchmarking framework for bioinformatics research.

Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

Panlineal is capable of generating Vgs from multiple genome alignments in form of lineal pan-genome. Combining short reads data, it can also detect the the allelism conduced by PAVs combinations of vast samples in a species.

A pipeline to run mapping, mash screen and assembly methods for pATLAS.

snakemake files of the tuxedo v2 pipeline from Pertea et al 2016

Script to obtain plasmid id from WGS data using bowtie2 to map