Short reads aligner for NIPT/CNV

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data

The complete sequence of a human genome

Tools (written in C using htslib) for manipulating next-generation sequencing data

A parallel wrapper for LTR_FINDER

Extensive de-novo TE Annotator

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

An integrated pipeline for identification of SSR markers

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

a hierarchical guided genome assembler

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

A single molecule sequence assembler for genomes large and small.

Rapid large-scale prokaryote pan genome analysis

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Developed for assemble the genomes with second-generation sequencing data, especially using the Illumina short reads. It is comparable to SOAPdenovo, and approach to SOAPdenovo2 in some aspects.

EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds.

GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be u…

A pipeline to de novo assemble the stLFR reads using Supernova Assembler

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Wiki form of BLAST documentation from NCBI

NCBI Prokaryotic Genome Annotation Pipeline

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Accurate sample inference from amplicon data with single nucleotide resolution

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

Find, circularise and annotate mitogenome from PacBio assemblies

hybrid assembly pipeline for bacterial genomes

Trinity RNA-Seq de novo transcriptome assembly