BOL: Related items

Kevler: Reference-free variant discovery in large eukaryotic genomes

Jit — Tue, 28 Jan 2020 03:21:53 -0600

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model.

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

Perl Special Vars Quick Reference

Abhimanyu Singh — Tue, 07 Feb 2017 05:08:47 -0600

`$_`	The default or implicit variable.
`@_`	Subroutine parameters.
`$a` `$b`	sort comparison routine variables.
`@ARGV`	The command-line args.
Regular Expressions
`$`	Regexp parenthetical capture holders.
`$&`	Last successful match (degrades performance).
`${^MATCH}`	Similar to `$&` without performance penalty. Requires /p modifier.
$`	Prematch for last successful match string (degrades performance).
`${^PREMATCH}`	Similar to $` without performance penalty. Requires `/p` modifier.
`$'`	Postmatch for last successful match string (degrades performance).
`${^POSTMATCH}`	Similar to `$'` without performance penalty. Requires `/p` modifier.
`$+`	Last paren match.
`$^N`	Last closed paren match (last submatch).
`@+`	Offsets of ends of successful submatches in scope.
`@-`	Offsets of starts of successful submatches in scope.
`%+`	Like `@+`, but for named submatches.
`%-`	Like `@-`, but for named submatches.
`$^R`	Last regexp (?{code}) result.
`${^RE_DEBUG_FLAGS}`	Current value of regexp debugging flags. See `use re 'debug';`
`${^RE_TRIE_MAXBUF}`	Control memory allocations for RE optimizations for large alternations.
Encoding
`${^ENCODING}`	The object reference to the Encode object, used to convert the source code to Unicode.
`${^OPEN}`	Internal use: \0 separated Input / Output layer information.
`${^UNICODE}`	Read-only Unicode settings.
`${^UTF8CACHE}`	State of the internal UTF-8 offset caching code.
`${^UTF8LOCALE}`	Indicates whether UTF8 locale was detected at startup.
IO and Separators
`$.`	Current line number (or record number) of most recent filehandle.
`$/`	Input record separator.
`$\|`	Output autoflush. 1=autoflush, 0=default. Applies to currently selected handle.
`$,`	Output field separator (lists)
`$\`	Output record separator.
`$"`	Output list separator. (interpolated lists)
`$;`	Subscript separator. (Use a real multidimensional array instead.)
Formats
`$%`	Page number for currently selected output channel.
`$=`	Current page length.
`$-`	Number of lines left on page.
`$~`	Format name.
`$^`	Name of top-of-page format.
`$:`	Format line break characters
`$^L`	Form feed (default "\f").
`$^A`	Format Accumulator
Status Reporting
`$?`	Child error. Status code of most recent system call or pipe.
`$!`	Operating System Error. (What just went 'bang'?)
`%!`	Error number hash
`$^E`	Extended Operating System Error (Extra error explanation).
`$@`	Eval error.
`${^CHILD_ERROR_NATIVE}`	Native status returned by the last pipe close, backtick (`` ) command, successful call to wait() or waitpid(), or from the system() operator.
ID's and Process Information
`$$`	Process ID
`$<`	Real user id of process.
`$>`	Effective user id of process.
`$(`	Real group id of process.
`$)`	Effective group id of process.
`$0`	Program name.
`$^O`	Operating System name.
Perl Status Info
`$]`	Old: Version and patch number of perl interpreter. Deprecated.
`$^C`	Current value of flag associated with -c switch.
`$^D`	Current value of debugging flags
`$^F`	Maximum system file descriptor.
`$^I`	Value of the -i (inplace edit) switch.
`$^M`	Emergency Memory pool.
`$^P`	Internal variable for debugging support.
`$^R`	Last regexp (?{code}) result.
`$^S`	Exceptions being caught. (eval)
`$^T`	Base time of program start.
`$^V`	Perl version.
`$^W`	Status of -w switch
`${^WARNING_BITS}`	Current set of warning checks enabled by `use warnings;`
`$^X`	Perl executable name.
`${^GLOBAL_PHASE}`	Current phase of the Perl interpreter.
`$^H`	Internal use only: Hook into Lexical Scoping.
`%^H`	Internaluse only: Useful to implement scoped pragmas.
`${^TAINT}`	Taint mode read-only flag.
`${^WIN32_SLOPPY_STAT}`	If true on Windows `stat()` won't try to open the file.
Command Line Args
`ARGV`	Filehandle iterates over files from command line (see also `<>`).
`$ARGV`	Name of current file when reading <>
`@ARGV`	List of command line args.
`ARGVOUT`	Output filehandle for -i switch
Miscellaneous
`@F`	Autosplit (-a mode) recipient.
`@INC`	List of library paths.
`%INC`	Keys are filenames, values are paths to modules included via `use, require,` or `do`.
`%ENV`	Hash containing current environment variables
`%SIG`	Signal handlers.
`$[`	Array and substr first element (Deprecated!).

See perlvar for detailed descriptions of each of these (and a few more) special variables.

CLA: Contig-Layout-Authenticator

Jit — Fri, 05 May 2017 05:58:36 -0500

To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

Script https://sourceforge.net/projects/c-l-authenticator/files/

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155459

RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler

Jit — Sat, 04 Jan 2020 01:08:09 -0600

RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. The updated version of RePS incorporates some of the ideas introduced by Phusion on clustering

More at

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC186573/

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/ricedb/Tools/RePS/RePS-IBM-AIX.tar.gz

Unicycler: Hybrid assembly pipeline for bacterial genomes

Jit — Fri, 10 Nov 2017 03:58:27 -0600

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

Address of the bookmark: https://github.com/rrwick/Unicycler

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Jit — Tue, 15 May 2018 07:35:26 -0500

HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccurate performance on others. With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technologies, including but not limited to: NGS short reads (Illumina HiSeq) clone-based sequencing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X Genomics Linked-Reads proximity-ligation (Hi-C) reads high-coverage sequencing (>40x coverage-per-SNP) using above technologies combinations of the above technologies (e.g. scaffold long reads with Hi-C reads) See below for specific examples of command line options and best practices for some of these technologies. NOTE: At this time HapCUT2 is for diploid organisms only. VCF input should contain diploid variants. If you use HapCUT2 in your research, please cite: Edge, P., Bafna, V. & Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:10.1101/gr.213462.116

Address of the bookmark: https://github.com/vibansal/HapCUT2

transrate: Understanding your transcriptome assembly

Neel — Fri, 13 Jul 2018 07:49:26 -0500

Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.

Address of the bookmark: http://hibberdlab.com/transrate/index.html

SvABA: Genome-wide detection of structural variants and indels by local assembly

Abhimanyu Singh — Mon, 21 Jan 2019 17:58:56 -0600

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

NextDenovo: string graph-based de novo assembler for TGS long reads

Jit — Sun, 05 Jan 2020 04:08:29 -0600

NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is about 97-98%, to further improve single base accuracy, please use NextPolish.

NextDenovo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be used to construct a string graph with corrected reads. It also contains a modified version of minimap2 for adapting input and output and producing more sensitive and accurate dovetail overlaps, and some useful utilities (see here for more details).

Address of the bookmark: https://github.com/Nextomics/NextDenovo

MEC: Contig Misassembly Correction

BioStar — Tue, 04 Feb 2020 23:40:49 -0600

MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the statistical analysis of GC-contents. We apply MEC to four real contig datasets, and carry out experiments to analyze the influence of MEC on scaffolding results, which shows that MEC can reduce misassemblies effectively and result in quantitative improvements in scaffolding quality. MEC is publicly available for download at https://github.com/bioinfomaticsCSU/MEC.

Address of the bookmark: https://github.com/bioinfomaticsCSU/MEC