Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak

As high-throughput sequencing technologies are becoming more widely adopted for analysing pathogens in disease outbreaks there needs to be assurance that the different sequencing technologies and approaches to data analysis will yield reliable and comparable results. Conversely, understanding where agreement cannot be achieved provides insight into the limitations of these approaches and also allows efforts to be focused on areas of the process that need improvement. This manuscript describes the next-generation sequencing of three closely related viruses, each analysed using different sequencing strategies, sequencing instruments and data processing pipelines. In order to determine the comparability of consensus sequences and minority (sub-consensus) single nucleotide variant (mSNV) identification, the biological samples, the sequence data from 3 sequencing platforms and the *.bam quality-trimmed alignment files of raw data of 3 influenza A/H5N8 viruses were shared. This analysis demonstrated that variation in the final result could be attributed to all stages in the process, but the most critical were the well-known homopolymer errors introduced by 454 sequencing, and the alignment processes in the different data processing pipelines which affected the consistency of mSNV detection. However, homopolymer errors aside, there was generally a good agreement between consensus sequences that were obtained for all combinations of sequencing platforms and data processing pipelines. Nevertheless, minority variant analysis will need a different level of careful standardization and awareness about the possible limitations, as shown in this study

Intentions on desired length of stay among immigrants in Italy

Abstract The decision to emigrate from the country of origin may not be a permanent one: migrants can decide to return home or to emigrate to a third country. This phenomenon, established for some time in certain other European countries, has become an important one for Italy only recently. This paper contributes to the knowledge of migrants’ intentions in two ways: on the one hand, it analyses the factors associated with indecision about future plans; on the other, it focuses on the desired length of stay and its relationship with attachments (family, economic, socio-cultural and psychological) to host and home country. We used two logistic regression models: one for migrants’ indecision and the other for migrants’ desired length of stay. The data were collected by survey, coordinated by the ISMU Foundation and conducted in 2008 and 2009 with more than 12,000 migrants living in Italy. According to our results, indecision seems to be associated with an intermediate phase of migration at the early stage of family development in the case of negative balance of the migration experience, while attachment to the host country is associated with longer stay, and no attachments or attachment to the country of origin are associated with shorter stay

Beyond the ‘Migrant Network’? Exploring assistance received in the migration of brazilians to Portugal and the Netherlands

This paper explores the tenability of three important critiques to the ‘migrant network’ approach in migration studies: (1) the narrow focus on kin and community members, which connect prospective migrants in origin countries with immigrants in the destination areas, failing to take due account of sources of assistance beyond the ‘migrant network’ like institutional or online sources; (2) that it is misleading to assume a general pattern in the role of migrant networks in migration, regardless of contexts of arrival or departure, including the scale and history of migration or the immigration regime; and (3) that ‘migrant networks’ are not equally relevant to all migrants, and that important differences may exist between labour migrants and other types of migrants like family migrants or students. Drawing on survey data on the migration of Brazilians to Portugal and the Netherlands we find support for these critiques but also reaffirm the relevance of ‘migrant networks’.info:eu-repo/semantics/publishedVersio