Sequence alignment tools
Parse and process SAM and BAM formatted files
Datastores for reads, not your papa's FASTQ 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
Genomic data manipulation tool
parsing SAM files to extract chimeric alignments and report each chimeric locus with its supporting reads
FLiCK - Format LeveragIng Compression frameworK
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
This repository streamlines the conversion of raw DNA sequencing data from FASTQ to BAM format, incorporating scripts that not only facilitate BAM conversion but also generate Sequence Alignment Map (SAM) files.
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