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- PersonalGenomes@Home (section Alignment with Bowtie)typically about 2.2 GB for the human genome. See also: Bowtie paper in Genome Biology. We have used bowtie with its default settings to align the PGP2 data from...14 KB (11 words) - 21:03, 1 July 2009
- existing genomic sequence SOAP suite of programs, no de novo assembly (yet). Bowtie "fast and memory efficient" The most complete list to date is @seqanswers...4 KB (436 words) - 22:34, 12 February 2010
- authors with version 1.3.0) bowtie (works with 0.12.7) Also completes running example with Python 2.7.1rc1, numpy-1.5.1 and bowtie 0.12.7 on in-house data...12 KB (1,677 words) - 09:50, 30 September 2014
- Raw sequences are pre-processed and aligned using various options (BWA or Bowtie). The GeZnome Analysis Took Kit (GATK) and SAMtools are used to call variants...9 KB (431 words) - 20:34, 29 October 2018
- 2009;10(3):R25. DOI:10.1186/gb-2009-10-3-r25 | PubMed ID:19261174 | HubMed [bowtie] Trapnell C, Pachter L, and Salzberg SL. TopHat: discovering splice junctions...7 KB (1,429 words) - 23:31, 4 April 2012
- tree) as a constraint in RAXML Martin: used phyML for whole genome tree Try bowtie? only for human... JE: ask Sanderson's group Any reason not to use a guide...2 KB (285 words) - 21:53, 17 August 2017
- on protein family covariation Humann2 First maps reads to reference db (bowtie), then homology search with higher sensitivity Two steps for computational...824 bytes (110 words) - 20:06, 7 August 2017
- Oligonucleotide Analysis Package. MAQ - Mapping and Assembly with Qualities. Bowtie - Bowtie. An ultrafast, memory-efficient short read aligner. BWA - Burrows-Wheeler...5 KB (463 words) - 20:17, 20 June 2012
- Oligonucleotide Analysis Package. MAQ - Mapping and Assembly with Qualities. Bowtie - Bowtie. An ultrafast, memory-efficient short read aligner. BWA - Burrows-Wheeler...8 KB (650 words) - 00:46, 6 June 2012
- suffix arrays Previously used for aligning short reads to genomes (BWA, Bowtie) Recently applied to assembly (extension of SGA assembler, really sped it...2 KB (309 words) - 17:39, 7 August 2017
- users to get their data faster. Release Notes 1.0.2 (08/19/2013) Switch from Bowtie to BWA for default alignments for generating SAM files. The BWA version...13 KB (1,993 words) - 15:21, 14 December 2022
- is available on the MAQ page. Bowtie - The Burge Lab is currently analyzing the quality of reads mapped using Bowtie. Bowtie is believed to be MUCH faster...16 KB (2,411 words) - 19:14, 13 January 2011
- bwa_map_050 and another 30 jobs bowtie_map_001 to bowtie_map_030. We want to remove all our still running or submitted and waiting bowtie_map jobs, but do not touch...44 KB (7,302 words) - 15:55, 27 November 2013
- 2.27(default) fasta/35.4.12(default) muscle/3.8.31(default) tabix/0.2.6 bowtie/2.0.0b3(default) freec/5.7(default) novoalign/2.08.03(default) tmhmm/2.0c(default)...9 KB (1,186 words) - 18:07, 14 December 2022
- reference_seq.fa.gz bowtie_reference_seq Let's create an output directory: $ mkdir BAM Now, let's get parallel: $ parallel "bowtie2 -x bowtie_reference_seq -U...33 KB (4,704 words) - 14:18, 27 September 2017
- /home/oeil/trunk/tmp BowtieToBedFormat: [mkdir] Created dir: /home/oeil/trunk/tmp [jar] Building jar: /home/oeil/trunk/jars/fp4/BowtieToBedFormat.jar [delete]...3 KB (0 words) - 00:20, 27 September 2017
- /home/heather/trunk/tmp BowtieToBedFormat: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/BowtieToBedFormat.jar [delete]...3 KB (0 words) - 00:20, 27 September 2017
- /home/heather/trunk/tmp BowtieToBedFormat: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/conversion_util/BowtieToBedFormat...15 KB (0 words) - 00:32, 27 September 2017
- worse indexing fasta with samtools is not the same as indexing with bwa, bowtie etc. mapping This is often the longest step, with options specific for each...18 KB (3,066 words) - 08:48, 20 September 2014
- multiple times to the mouse genome (mm9) are shown. Reads were aligned with Bowtie. NuGen samples show an increase in non-aligned reads at low input amounts...9 KB (288 words) - 00:49, 20 June 2012
