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

Collecting Genotypes from ENA and make their SNPs

Get sex info from BAM file

For comparing the subgenomes of wheat

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

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

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).

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

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

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

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.

Parses Samtools output and extracts flagstat results such as number of reads that are pass/fail that are properly aligned, etc.

Variant caller from pileup notation / samtools alignment

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

Python implementation of htslib supporting BAM, SAM, and BGZF compression

A public, web-based homozygosity mapping tool