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samtools view -h -b sample_sorted.bam "chr1:10-13" > tiny_sorted.bam Extract the same reads as above, but instead of displaying them, writes them to a new bam file, tiny_sorted.bam . The -b option makes the output compressed and the -h option causes the SAM headers to be output also.
Velvet is an algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments.This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the removal of errors and the simplification of repeated regions. [2]
MEGA has created captions using the Real-Time Caption Editor to be able to analyze the properties of the results of the phylogenetic tree. This allows a user to be able to follow and interpret final results. [14] The Caption Expert is a part of MEGA which provides publication-like detailed captions based on the properties of analysis results.
Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ). DNA: Hepperle D (www.sequentix.de) 2020 Genoogle Genoogle uses indexing and parallel processing techniques for searching DNA and Proteins sequences. It is developed in Java and open source. Both: Albrecht F: 2015 HMMER
Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translation ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred
DNA Master is a free software tool that students can download on a Windows computer that utilizes the programs GLIMMER, GeneMark, Aragorn, and tRNAscan-SE to auto-annotate a genome that is uploaded as a FASTA format file. [3]
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Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files.