BOL: Related items

AMStat: display statistics of large sequence files from next generation sequencing projects

Neel — Fri, 09 Nov 2018 13:34:56 -0600

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

Address of the bookmark: http://samstat.sourceforge.net/

FiNGS: Filters for Next Generation Sequencing

Neel — Sat, 27 Feb 2021 01:18:35 -0600

Key features

Filters SNVs from any variant caller to remove false positives
Calculates metrics based on BAM files and provides filtering not possible with other tools
Fully user-configurable filtering (including which filters to use and their thresholds)
Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

Hapsembler: An Assembler for Highly Polymorphic Genomes

Jit — Tue, 22 May 2018 04:09:53 -0500

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/

Address of the bookmark: http://compbio.cs.toronto.edu/hapsembler/

PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.

Surabhi Chaudhary — Mon, 11 Jun 2018 03:08:26 -0500

We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler. http://derisilab.ucsf.edu/software/price/

Address of the bookmark: http://derisilab.ucsf.edu/software/price/

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data

Rahul Nayak — Tue, 03 Jul 2018 04:14:52 -0500

ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm also detects base substitutions in transcript sequences corresponding to sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are reported as splice graphs in dot output format.

Address of the bookmark: https://github.com/bcgsc/ChopStitch

FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads

Jit — Mon, 20 Aug 2018 04:08:50 -0500

Here is the command to run the tool:

python finisherSC.py destinedFolder mummerPath

If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.

python finisherSC.py -par 20 destinedFolder mummerPath

Sometimes, if the names of raw reads and contigs consists of special characters/formats, FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command.

    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' raw_reads.fasta > newRaw_reads.fasta
    cp newRaw_reads.fasta raw_reads.fasta
    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' contigs.fasta > newContigs.fasta
    cp newContigs.fasta contigs.fasta

Address of the bookmark: https://github.com/kakitone/finishingTool

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

Jit — Fri, 24 Jan 2020 04:09:15 -0600

MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. MitoZ is available from https://github.com/linzhi2013/MitoZ.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

PAired-eND Assembler for DNA sequences

Neel — Wed, 06 Apr 2016 05:25:34 -0500

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

More at https://github.com/neufeld/pandaseq

Address of the bookmark: https://github.com/neufeld/pandaseq

REAPR: a universal tool for genome assembly evaluation

Jitendra Prajapati — Wed, 06 Apr 2016 18:26:31 -0500

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.

http://www.sanger.ac.uk/science/tools/reapr

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-5-r47