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• Reference Indexes
  ...rence indexes built for the respective tools using the appropriate genomic sequence data. This page provides a short overview of our reference index building p ...most reference indexes to be built. In that case we'll use the non-masked sequence.
  2 KB (361 words) - 20:30, 12 August 2022
• Consed
  calling, sequence comparisons, and sequence assembly. Phred, Cross_match, Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the
  3 KB (348 words) - 18:39, 12 August 2022
• UCSC
  ...ion tasks such as reverse complementation, codon and amino acid lookup and sequence translation, as well as functions specifically designed for extracting, loa
  3 KB (349 words) - 20:53, 12 August 2022
• WGS Assembler
  ...n sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celer
  3 KB (359 words) - 20:56, 12 August 2022
• SRAssembler
  ...cal assembly of genomic regions matching a homologous query protein or DNA sequence. ...ssembler first collects the reads that can be locally aligned to the query sequence and assembles them into contigs. Additional reads are then found by alignin
  3 KB (381 words) - 15:33, 27 May 2022
• Kalign
  Kalign is a fast multiple sequence alignment program for biological sequences. "Kalign 3: multiple sequence alignment of large data sets."
  2 KB (265 words) - 19:28, 12 August 2022
• USEARCH
  ...tions, including E-values, identity, coverage (fraction of query or target sequence covered by the alignment) and maximum gap length, and a range of output fil ...RCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude
  4 KB (559 words) - 17:19, 22 August 2022
• PRINSEQ
  ...n in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
  2 KB (271 words) - 15:52, 10 June 2022
• Wgs
  ...n sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celer
  3 KB (375 words) - 20:55, 12 August 2022
• Nt
  This repo contains a set of neural transducer, e.g. sequence-to-sequence model, focusing on character-level tasks. It powers several papers and work
  2 KB (262 words) - 14:38, 15 July 2022
• MHAP
  ...rithm. Designed to efficiently detect all overlaps between noisy long-read sequence data. It efficiently estimates Jaccard similarity by compressing sequences
  2 KB (270 words) - 16:15, 10 June 2022
• SEQPower
  SEQPower provides statistical power analysis and sample size estimation for sequence-based association studies. ...tez, B. Peng and S. M. Leal, Power analysis and sample size estimation for sequence-based association studies. Bioinformatics. (2014)]
  2 KB (274 words) - 22:38, 21 August 2022
• GHOST-MP
  ...ches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX. GHOST-MP runs on a distributed memory system and proc
  2 KB (285 words) - 20:11, 7 May 2020
• Shasta
  ...of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer re
  3 KB (402 words) - 21:24, 6 December 2019
• Ont tutorial cas9
  ...t enrichment strategy. This workflow is suitable for Oxford Nanopore fastq sequence collections and requires a reference genome and a BED file of target coordi
  2 KB (289 words) - 18:38, 2 June 2022
• Tcoffee
  T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine th T-Coffee: A novel method for multiple sequence alignments.
  2 KB (280 words) - 20:46, 12 August 2022
• NCBI GenBank Tools
  ..., 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), t
  2 KB (291 words) - 14:33, 19 August 2022
• ProDy
  ...s for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well
  2 KB (294 words) - 19:38, 21 August 2022
• Newbler
  ...de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454
  2 KB (305 words) - 16:17, 19 August 2022
• Rvtests
  ...tests, is a flexible software package for genetic association analysis for sequence datasets. ...ficient and Comprehensive Tool for Rare Variant Association Analysis Using Sequence Data. Bioinformatics 2016 32: 1423-1426.]
  3 KB (293 words) - 21:59, 21 August 2022

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