Editing Sequence assembly (section)

== Programs ==

For a lists of ''de-novo'' assemblers, see [[De novo sequence assemblers]]. For a list of mapping aligners, see [[List of sequence alignment software#Short-read sequence alignment|List of sequence alignment software § Short-read sequence alignment]].

Some of the common tools used in different assembly steps are listed in the following table:
{| class="wikitable"
|+Sequence Assembly Tools
!Software
!Read type
!Tool web page
!Notes
|-
|FastQC
|Multiple
|https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|This is a common tool used to check reads quality from different sequencing technologies such as [[Illumina, Inc.|Illumina]], [[454 Life Sciences|454]], and [[Pacific Biosciences|PacBio]]. 
|-
|BWA
|Short & Long reads
|https://sourceforge.net/projects/bio-bwa/files/
|This is a [[Command-line interface|command line]] tool. Mostly known for lightweight run and accurate sequence alignment. 
|-
|MiniMap2
|Long reads 
|https://github.com/lh3/minimap2
|This command line tool is designed to handle [[Pacbio|PacBio]] & [[Oxford Nanopore Technologies|Oxford Nanopore]] and reads with 15% error rate. 
|-
|bwa-mem2
|Short & Long reads
|https://github.com/bwa-mem2/bwa-mem2
|This command line tool is a performance optimized development, and drop-in replacement, of the BWA program.<ref>{{Cite book |last1=Vasimuddin |first1=Md. |last2=Misra |first2=Sanchit |last3=Li |first3=Heng |last4=Aluru |first4=Srinivas |chapter=Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems |date=May 2019 |title=2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) |chapter-url=https://ieeexplore.ieee.org/document/8820962 |publisher=IEEE |pages=314–324 |doi=10.1109/IPDPS.2019.00041 |arxiv=1907.12931 |isbn=978-1-7281-1246-6}}</ref>
|-
|bwa-meme
|Short & Long reads
|https://github.com/kaist-ina/BWA-MEME
|This command line tool is a performance optimized development, and drop-in replacement, of the bwa-mem2 algorithm utilizing Machine Learning.<ref>{{Cite journal |last1=Jung |first1=Youngmok |last2=Han |first2=Dongsu |date=2022-03-07 |title=BWA-MEME: BWA-MEM emulated with a machine learning approach |url=https://academic.oup.com/bioinformatics/article/38/9/2404/6543607 |journal=Bioinformatics |volume=38 |issue=9 |pages=2404–2413 |doi=10.1093/bioinformatics/btac137 |pmid=35253835 |issn=1367-4803}}</ref>
|-
|LoReTTA
|Long reads 
|https://github.com/salvocamiolo/LoReTTA/releases/tag/v0.1
|This tool is designed to assemble (reference-guided) viral genomes at a greater accuracy using PacBio CCS reads.
|-
|[[SPAdes (software)|SPAdes]]
|Short & Long reads 
|http://cab.spbu.ru/software/spades/
|This is an assembly tool that runs on the command line.  
|-
|[[Samtools]]
|Alignment analysis
|https://samtools.github.io
|This is useful post-assembly. It can generate different statistics and perform multiple filtering steps to the alignment file. 
|}