BOL: Results for "Contig"

Results for "Contig"

- Rahul Nayak@rahul
String graph based genome assembly software and tools !
...rrors in the reads. The second phase assembles contigs from the corrected reads. Th.../or mate pair data to build scaffolds from the contigs. The output of this software...Such consensus sequences are then extended to contigs. BASE is a practically...
2329 days ago
- Surabhi Chaudhary@surabhi
BBTools for bioinformatician !
...-reference-sequence level, so if a bacterial assembly has more than one contig, you may want to glue them to...e cases for generating a fake LMP library for scaffolding from a set of contigs. Read 1 will be from the lef...
2271 days ago
+2 more Blogs

- Jit@jit.aber
Bioinformatics Scripts
Some of the useful bioinformatics scripts. For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly. http://milkweedgenome.org/?q=scripts
3361 days ago
- Jit@jit.aber
HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding
HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo ev...
1093 days ago
+37 more Bookmarks

- Jit@jit.aber
Download blasr 1.3 version
...be/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2Illegal divis...on closed filehandle FILE at bin/OPERA-long-read.pl line 250.rm anchor_contig_info.dat contig_length.dat fi...
2152 days ago

- Jit@jit.aber
Genome Assembly Tools and Software - PART2 !!
..., it is capable of assembling contigs together to form more comple...lds that order and orient the contigs. The updated version of RePS...C++ based tool for assembling contigs and/or scaffolds to full chr...ies novel transfrags with DNA contigs or genes of close related sp...
2686 days ago

- Jit@jit.aber
Genome Assembly Tools and Software - PART1 !!
...[2] to extend seed reads (or contigs generated by another assembler) into longer contigs, by iteratively calling Vmat...for analyzing ABySS-assembled contigs from shotgun transcriptome d...rogram for sequence assembly, contig editing, and mutation detecti...
2686 days ago
- Rahul Nayak@rahul
Bioinformatics OneLiner
...duplicated lines: awk '!seen[$0]++' To sum assembly size from SPAdes contigs.fasta or scaffolds.fasta fil...le_1.fq) | cut -f 5-8 | \tr "\t" "\n" > myf2.fq To filter and sort contig identifiers from SPAdes assem...
2218 days ago
+3 more Top-level pages

- Jit@jit.aber
All about #newbler #assembly https://contig.wordpress.com/ #NGS
2531 days ago
- Jit@jit.aber
#N50 = contig length so that half of the contigs are longer and 1/2 of contigs are shorter
2179 days ago

- Rahul Nayak@rahul
Phased Human Genome Assembly !
...ained in gapless sequence at least 27 Mb long. The primary contig assembly is 2.89 Gb long and consists of 865 contigs that were assembled with Pac...te: Blog post: Data Release: Highest-Quality, Most Contiguous Individual Human Genome A...
2036 days ago

- Jit@jit.aber
Perl script to insert sequence in contig !!
# sub signature: #insertSEQintoCONTIGatLOC( SEQ , CONTIG , LOC ) ; sub insertSEQintoCONTIGatLOC{ my ( $SEQ , $CONTIG , $LOC ) = @_; substr( $CON...print 'insert = '.($s = insertSEQintoCONTIGatLOC( "CCCC ", $s , 26 ))."\n...
2709 days ago
- Rahul Nayak@rahul
Create a heatmap with R
bio
2470 days ago
+9 more Bio-Scripts

- Neelam Jha@neelam
Comment on "REAPR: a universal tool for genome assembly evaluation"
...to each other. The program will also break up contigs/scaffolds at spurious sites to form smaller (but hopefully correct) contigs. Reapr runs pretty slowly, s...the command is the potential problems with the contig names. If you run into any pr...
1337 days ago
- Jit@jit.aber
Comment on "MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)"
➜ mashmap-Linux64-v2.0 git:(master) ✗ ./mashmap -h-----------------Mashmap is an approximate long read or contig mapper based on Jaccardsimilarity-----------------Example usage:$ mash...
2123 days ago
+2 more Comments