Sequence alignment tools
Parse and process SAM and BAM formatted files
Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts
Datastores for reads, not your papa's FASTQ files.
Genomic data manipulation tool
FLiCK - Format LeveragIng Compression frameworK
parsing SAM files to extract chimeric alignments and report each chimeric locus with its supporting reads
🧬 Automating the functionality of open-source program Minimap2
This repository contains a Python-based genome assembler designed to perform k-mer spectrum-based error correction and generate SAM files for visualizing genome mappings. It supports genomic data analysis with a focus on identifying mutations relevant to antibiotic resistance.
SAMtools and BCFtools (v1.10) for manipulating next-generation sequencing data, from bioconda
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