DNALinux

Suite of programs for interacting with high-throughput sequencing data. Home: https://www.htslib.org

Biopython is a set of freely available tools for biological computation written in Python

Ultrafast, memory-efficient and highly accurate pair-end read merger

the antibiotics and Secondary Metabolite Analysis SHell

De novo assembler for single-cell, isolate, RNA, plasmid genomes and metagenomes

All in one FASTQ preprocessor

Conduct quality control of raw sequence data

The SRA Toolkit and SDK from NCBI is a collection of tools for using data in the INSDC SRA

The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa.

Sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

Mapping low-divergent sequences against a larger reference genome

Convert bedGraph to bigWig file

Design PCR primers from DNA sequence.

Screening DNA sequences for interspersed repeats and low complexity sequences

Integrates long reads for the detection of SNPs/indels from long-read sequencing data

Python precompiled with no-GIL (aka free-threading)

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

count k-mers in DNA sequences

KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model.